Starting phenix.real_space_refine on Wed Mar 4 03:57:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kai_22771/03_2026/7kai_22771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kai_22771/03_2026/7kai_22771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kai_22771/03_2026/7kai_22771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kai_22771/03_2026/7kai_22771.map" model { file = "/net/cci-nas-00/data/ceres_data/7kai_22771/03_2026/7kai_22771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kai_22771/03_2026/7kai_22771.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 sd= 0.036 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 42 5.16 5 C 6979 2.51 5 N 1807 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10718 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3310 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 416} Chain breaks: 3 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 65 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: "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: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3864 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 28, 'TRANS': 463} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 86 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: {'GLU:plan': 3, 'GLN:plan1': 1, '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 Chain: "G" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 280 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'UNK:plan-1': 56} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 2.22, per 1000 atoms: 0.21 Number of scatterers: 10718 At special positions: 0 Unit cell: (110.67, 124.95, 139.23, 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 42 16.00 O 1890 8.00 N 1807 7.00 C 6979 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 - 3.00 Amino acid : True - 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: 0.83 Conformation dependent library (CDL) restraints added in 600.4 milliseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 69.6% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.535A pdb=" N GLY A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.528A pdb=" N LYS A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.574A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 214 through 225 removed outlier: 3.621A pdb=" N ARG A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 4.054A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.736A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.959A pdb=" N MET A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 341 through 347 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.584A pdb=" N ALA A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.628A pdb=" N THR A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.530A pdb=" N TYR A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.762A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.892A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 64 removed outlier: 4.274A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 removed outlier: 3.627A pdb=" N PHE D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 112 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.778A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.742A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.714A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.540A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 294' Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 3.746A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.906A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 3.995A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 4.087A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.266A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.685A pdb=" N LYS D 493 " --> pdb=" O MET D 490 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 494 " --> pdb=" O MET D 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 490 through 494' Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.723A pdb=" N TYR E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 124 removed outlier: 3.676A 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: 4.011A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 3.954A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.270A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.505A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.851A 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 removed outlier: 3.512A pdb=" N GLY F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 72 removed outlier: 3.973A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN F 71 " --> pdb=" O LYS F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.546A pdb=" N LYS F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 Proline residue: F 103 - end of helix removed outlier: 3.834A 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: 3.732A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 174 through 192 removed outlier: 4.037A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 170 removed outlier: 3.512A pdb=" N UNK G 165 " --> pdb=" O UNK G 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK G 166 " --> pdb=" O UNK G 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N UNK G 170 " --> pdb=" O UNK G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211 removed outlier: 3.668A pdb=" N ASN A 204 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284 Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.539A pdb=" N GLY A 327 " --> pdb=" O MET A 337 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436 removed outlier: 3.714A pdb=" N LYS D 432 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP D 434 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.533A pdb=" N TRP D 513 " --> pdb=" O ILE D 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 673 hydrogen bonds defined for protein. 1977 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: 1.85 Time building geometry restraints manager: 1.14 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: 3397 1.34 - 1.46: 2166 1.46 - 1.58: 5294 1.58 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 10924 Sorted by residual: bond pdb=" CA THR D 366 " pdb=" C THR D 366 " ideal model delta sigma weight residual 1.517 1.525 -0.009 1.02e-02 9.61e+03 7.16e-01 bond pdb=" CB LYS E 86 " pdb=" CG LYS E 86 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.42e-01 bond pdb=" CA LEU A 147 " pdb=" C LEU A 147 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.10e-02 2.27e+03 5.11e-01 bond pdb=" CG LEU F 129 " pdb=" CD2 LEU F 129 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.01e-01 bond pdb=" N LYS D 552 " pdb=" CA LYS D 552 " ideal model delta sigma weight residual 1.460 1.469 -0.010 1.42e-02 4.96e+03 4.58e-01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 14632 1.84 - 3.67: 154 3.67 - 5.51: 25 5.51 - 7.34: 7 7.34 - 9.18: 1 Bond angle restraints: 14819 Sorted by residual: angle pdb=" N GLU D 472 " pdb=" CA GLU D 472 " pdb=" CB GLU D 472 " ideal model delta sigma weight residual 113.65 110.47 3.18 1.47e+00 4.63e-01 4.69e+00 angle pdb=" CA SER D 220 " pdb=" C SER D 220 " pdb=" N PRO D 221 " ideal model delta sigma weight residual 118.44 121.62 -3.18 1.59e+00 3.96e-01 4.00e+00 angle pdb=" N ASN D 376 " pdb=" CA ASN D 376 " pdb=" C ASN D 376 " ideal model delta sigma weight residual 107.67 111.63 -3.96 2.09e+00 2.29e-01 3.59e+00 angle pdb=" N TRP D 14 " pdb=" CA TRP D 14 " pdb=" C TRP D 14 " ideal model delta sigma weight residual 109.81 113.96 -4.15 2.21e+00 2.05e-01 3.53e+00 angle pdb=" N ILE A 418 " pdb=" CA ILE A 418 " pdb=" C ILE A 418 " ideal model delta sigma weight residual 108.88 112.89 -4.01 2.16e+00 2.14e-01 3.45e+00 ... (remaining 14814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6123 17.84 - 35.69: 383 35.69 - 53.53: 52 53.53 - 71.37: 9 71.37 - 89.21: 12 Dihedral angle restraints: 6579 sinusoidal: 2511 harmonic: 4068 Sorted by residual: dihedral pdb=" CB GLU A 382 " pdb=" CG GLU A 382 " pdb=" CD GLU A 382 " pdb=" OE1 GLU A 382 " ideal model delta sinusoidal sigma weight residual 0.00 89.21 -89.21 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU D 472 " pdb=" CG GLU D 472 " pdb=" CD GLU D 472 " pdb=" OE1 GLU D 472 " ideal model delta sinusoidal sigma weight residual 0.00 88.17 -88.17 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU C 31 " pdb=" CG GLU C 31 " pdb=" CD GLU C 31 " pdb=" OE1 GLU C 31 " ideal model delta sinusoidal sigma weight residual 0.00 -87.78 87.78 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1112 0.029 - 0.058: 432 0.058 - 0.087: 142 0.087 - 0.116: 67 0.116 - 0.145: 16 Chirality restraints: 1769 Sorted by residual: chirality pdb=" CG LEU F 129 " pdb=" CB LEU F 129 " pdb=" CD1 LEU F 129 " pdb=" CD2 LEU F 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.26e-01 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 4.44e-01 chirality pdb=" CA ILE D 571 " pdb=" N ILE D 571 " pdb=" C ILE D 571 " pdb=" CB ILE D 571 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1766 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO F 48 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 14 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO D 15 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 15 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 15 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 317 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 318 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " -0.021 5.00e-02 4.00e+02 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1870 2.76 - 3.30: 10318 3.30 - 3.83: 16559 3.83 - 4.37: 18046 4.37 - 4.90: 33139 Nonbonded interactions: 79932 Sorted by model distance: nonbonded pdb=" OG1 THR A 201 " pdb=" OE1 GLU A 212 " model vdw 2.229 3.040 nonbonded pdb=" OG SER A 107 " pdb=" OD2 ASP A 110 " model vdw 2.289 3.040 nonbonded pdb=" O THR D 444 " pdb=" OG SER D 447 " model vdw 2.291 3.040 nonbonded pdb=" O TYR A 237 " pdb=" ND2 ASN A 243 " model vdw 2.294 3.120 nonbonded pdb=" O ILE F 28 " pdb=" ND2 ASN F 32 " model vdw 2.306 3.120 ... (remaining 79927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.560 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.060 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:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10924 Z= 0.132 Angle : 0.532 9.178 14819 Z= 0.279 Chirality : 0.039 0.145 1769 Planarity : 0.004 0.049 1850 Dihedral : 12.277 89.214 3935 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.22), residues: 1319 helix: 0.22 (0.17), residues: 804 sheet: -2.62 (0.45), residues: 89 loop : -2.47 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 99 TYR 0.012 0.001 TYR F 190 PHE 0.016 0.001 PHE D 547 TRP 0.010 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00295 (10924) covalent geometry : angle 0.53207 (14819) hydrogen bonds : bond 0.11410 ( 673) hydrogen bonds : angle 4.59961 ( 1977) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.413 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1155 time to fit residues: 14.3686 Evaluate side-chains 63 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 394 GLN D 307 GLN D 330 HIS E 88 HIS F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049392 restraints weight = 41063.050| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.03 r_work: 0.2768 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10924 Z= 0.171 Angle : 0.544 12.392 14819 Z= 0.269 Chirality : 0.039 0.169 1769 Planarity : 0.004 0.049 1850 Dihedral : 3.367 17.926 1477 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.45 % Allowed : 8.98 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1319 helix: 1.53 (0.19), residues: 798 sheet: -2.12 (0.46), residues: 89 loop : -1.90 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 110 TYR 0.013 0.001 TYR F 190 PHE 0.023 0.001 PHE A 94 TRP 0.006 0.001 TRP A 380 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00408 (10924) covalent geometry : angle 0.54431 (14819) hydrogen bonds : bond 0.04129 ( 673) hydrogen bonds : angle 3.60562 ( 1977) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.7089 (ptm) cc_final: 0.6805 (tmm) REVERT: A 90 MET cc_start: 0.8348 (tpp) cc_final: 0.7499 (tpp) REVERT: A 94 PHE cc_start: 0.9393 (t80) cc_final: 0.8981 (m-10) REVERT: A 135 MET cc_start: 0.7404 (mmp) cc_final: 0.7157 (mmm) REVERT: A 337 MET cc_start: 0.8148 (ppp) cc_final: 0.7840 (pmm) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.0872 time to fit residues: 9.4535 Evaluate side-chains 65 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain F residue 129 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 17 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS E 72 HIS F 45 ASN F 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.064043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.046910 restraints weight = 42017.830| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.99 r_work: 0.2716 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 10924 Z= 0.306 Angle : 0.649 12.365 14819 Z= 0.327 Chirality : 0.043 0.171 1769 Planarity : 0.004 0.050 1850 Dihedral : 3.760 19.583 1477 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.35 % Allowed : 12.03 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.24), residues: 1319 helix: 1.74 (0.19), residues: 799 sheet: -1.82 (0.47), residues: 91 loop : -1.69 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 313 TYR 0.016 0.002 TYR F 190 PHE 0.019 0.002 PHE D 547 TRP 0.010 0.001 TRP D 14 HIS 0.004 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00739 (10924) covalent geometry : angle 0.64936 (14819) hydrogen bonds : bond 0.05387 ( 673) hydrogen bonds : angle 3.85125 ( 1977) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8400 (tpp) cc_final: 0.8147 (tpp) REVERT: A 135 MET cc_start: 0.7497 (mmp) cc_final: 0.7243 (mmm) REVERT: A 350 MET cc_start: 0.8684 (mmm) cc_final: 0.8152 (mmm) REVERT: D 516 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9032 (pp) REVERT: D 553 MET cc_start: 0.8329 (ttp) cc_final: 0.8091 (tmm) outliers start: 15 outliers final: 6 residues processed: 71 average time/residue: 0.0800 time to fit residues: 9.1048 Evaluate side-chains 64 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 129 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 134 optimal weight: 40.0000 chunk 90 optimal weight: 10.0000 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.066861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.050031 restraints weight = 41886.412| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.99 r_work: 0.2793 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10924 Z= 0.096 Angle : 0.493 10.805 14819 Z= 0.242 Chirality : 0.037 0.150 1769 Planarity : 0.003 0.050 1850 Dihedral : 3.298 15.619 1477 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.99 % Allowed : 13.29 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1319 helix: 2.28 (0.19), residues: 802 sheet: -1.54 (0.48), residues: 91 loop : -1.48 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 509 TYR 0.008 0.001 TYR F 190 PHE 0.008 0.001 PHE A 424 TRP 0.010 0.001 TRP E 131 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00205 (10924) covalent geometry : angle 0.49251 (14819) hydrogen bonds : bond 0.03175 ( 673) hydrogen bonds : angle 3.30399 ( 1977) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8414 (tpp) cc_final: 0.8177 (tpp) REVERT: C 43 ASP cc_start: 0.8689 (p0) cc_final: 0.8076 (p0) REVERT: F 153 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8611 (pp) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.0781 time to fit residues: 9.6910 Evaluate side-chains 67 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.063665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.046550 restraints weight = 41803.407| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.99 r_work: 0.2713 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10924 Z= 0.306 Angle : 0.652 12.049 14819 Z= 0.325 Chirality : 0.043 0.167 1769 Planarity : 0.004 0.050 1850 Dihedral : 3.686 19.174 1477 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.62 % Allowed : 14.99 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1319 helix: 2.12 (0.19), residues: 799 sheet: -1.55 (0.48), residues: 91 loop : -1.44 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 313 TYR 0.017 0.001 TYR F 190 PHE 0.015 0.002 PHE C 28 TRP 0.012 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00735 (10924) covalent geometry : angle 0.65210 (14819) hydrogen bonds : bond 0.05217 ( 673) hydrogen bonds : angle 3.76516 ( 1977) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8424 (tpp) cc_final: 0.8155 (tpp) REVERT: A 135 MET cc_start: 0.7424 (mmp) cc_final: 0.7160 (mmm) REVERT: C 43 ASP cc_start: 0.8546 (p0) cc_final: 0.7982 (p0) REVERT: D 516 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9021 (pp) REVERT: D 553 MET cc_start: 0.8189 (ttp) cc_final: 0.7973 (tmm) REVERT: F 153 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9007 (pp) outliers start: 18 outliers final: 10 residues processed: 73 average time/residue: 0.0868 time to fit residues: 10.0973 Evaluate side-chains 67 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 41 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 4 optimal weight: 0.0070 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.066581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.049847 restraints weight = 41745.123| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.98 r_work: 0.2787 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10924 Z= 0.097 Angle : 0.514 10.240 14819 Z= 0.250 Chirality : 0.038 0.151 1769 Planarity : 0.003 0.051 1850 Dihedral : 3.311 15.089 1477 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.99 % Allowed : 16.34 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1319 helix: 2.48 (0.19), residues: 799 sheet: -1.28 (0.48), residues: 91 loop : -1.24 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 509 TYR 0.007 0.001 TYR F 190 PHE 0.028 0.001 PHE A 94 TRP 0.011 0.001 TRP E 131 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00208 (10924) covalent geometry : angle 0.51427 (14819) hydrogen bonds : bond 0.03157 ( 673) hydrogen bonds : angle 3.31504 ( 1977) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.6872 (tmm) cc_final: 0.6188 (tmm) REVERT: A 90 MET cc_start: 0.8438 (tpp) cc_final: 0.8150 (tpp) REVERT: A 135 MET cc_start: 0.7248 (mmp) cc_final: 0.6925 (mmm) REVERT: A 350 MET cc_start: 0.8930 (mmm) cc_final: 0.8278 (mmm) REVERT: F 153 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8654 (pp) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.0879 time to fit residues: 9.9348 Evaluate side-chains 66 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.065806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.048990 restraints weight = 41896.109| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.98 r_work: 0.2762 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10924 Z= 0.128 Angle : 0.528 10.111 14819 Z= 0.259 Chirality : 0.038 0.207 1769 Planarity : 0.004 0.051 1850 Dihedral : 3.286 16.030 1477 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.35 % Allowed : 16.25 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1319 helix: 2.60 (0.19), residues: 798 sheet: -1.18 (0.48), residues: 91 loop : -1.22 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 90 TYR 0.013 0.001 TYR F 190 PHE 0.024 0.001 PHE A 94 TRP 0.008 0.001 TRP D 14 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00302 (10924) covalent geometry : angle 0.52773 (14819) hydrogen bonds : bond 0.03571 ( 673) hydrogen bonds : angle 3.33190 ( 1977) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.6974 (tmm) cc_final: 0.6286 (tmm) REVERT: A 90 MET cc_start: 0.8423 (tpp) cc_final: 0.8136 (tpp) REVERT: A 135 MET cc_start: 0.7336 (mmp) cc_final: 0.7015 (mmm) REVERT: C 40 LYS cc_start: 0.9109 (tttp) cc_final: 0.8810 (tttm) REVERT: F 49 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8761 (tm-30) REVERT: F 153 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8715 (pp) outliers start: 15 outliers final: 9 residues processed: 74 average time/residue: 0.0827 time to fit residues: 9.6727 Evaluate side-chains 70 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 23 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.066404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049658 restraints weight = 41640.955| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.98 r_work: 0.2782 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 : 0.002 0.041 10924 Z= 0.108 Angle : 0.527 9.716 14819 Z= 0.256 Chirality : 0.038 0.204 1769 Planarity : 0.003 0.048 1850 Dihedral : 3.207 15.205 1477 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 16.52 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.24), residues: 1319 helix: 2.69 (0.19), residues: 799 sheet: -1.03 (0.49), residues: 91 loop : -1.12 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 90 TYR 0.010 0.001 TYR F 190 PHE 0.028 0.001 PHE A 94 TRP 0.009 0.001 TRP E 131 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00249 (10924) covalent geometry : angle 0.52736 (14819) hydrogen bonds : bond 0.03221 ( 673) hydrogen bonds : angle 3.23738 ( 1977) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.6918 (tmm) cc_final: 0.6251 (tmm) REVERT: A 90 MET cc_start: 0.8446 (tpp) cc_final: 0.8148 (tpp) REVERT: C 40 LYS cc_start: 0.9077 (tttp) cc_final: 0.8779 (tttm) REVERT: F 49 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8701 (tm-30) REVERT: F 153 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8641 (pp) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.0823 time to fit residues: 9.8097 Evaluate side-chains 73 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 11 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.067256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.050563 restraints weight = 41499.981| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.98 r_work: 0.2808 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10924 Z= 0.094 Angle : 0.513 9.116 14819 Z= 0.246 Chirality : 0.037 0.197 1769 Planarity : 0.003 0.048 1850 Dihedral : 3.087 13.988 1477 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.81 % Allowed : 16.70 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.24), residues: 1319 helix: 2.81 (0.19), residues: 800 sheet: -0.86 (0.49), residues: 91 loop : -1.01 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 90 TYR 0.009 0.001 TYR F 190 PHE 0.026 0.001 PHE A 94 TRP 0.011 0.001 TRP E 131 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00210 (10924) covalent geometry : angle 0.51317 (14819) hydrogen bonds : bond 0.02863 ( 673) hydrogen bonds : angle 3.14974 ( 1977) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8422 (tpp) cc_final: 0.8116 (tpp) REVERT: A 135 MET cc_start: 0.7224 (mmp) cc_final: 0.6914 (mmm) REVERT: C 40 LYS cc_start: 0.9059 (tttp) cc_final: 0.8768 (tttm) REVERT: D 29 MET cc_start: 0.9063 (mtp) cc_final: 0.8841 (mtp) REVERT: F 49 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8722 (tm-30) REVERT: F 153 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8615 (pp) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.0827 time to fit residues: 9.5605 Evaluate side-chains 73 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 121 optimal weight: 6.9990 chunk 51 optimal weight: 0.0870 chunk 117 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 136 optimal weight: 50.0000 chunk 4 optimal weight: 0.3980 chunk 88 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.067018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.050306 restraints weight = 40692.566| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.01 r_work: 0.2827 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10924 Z= 0.091 Angle : 0.511 8.437 14819 Z= 0.245 Chirality : 0.037 0.196 1769 Planarity : 0.003 0.047 1850 Dihedral : 2.982 13.584 1477 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.90 % Allowed : 16.70 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.24), residues: 1319 helix: 2.89 (0.19), residues: 801 sheet: -0.71 (0.50), residues: 91 loop : -0.87 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 90 TYR 0.009 0.001 TYR F 190 PHE 0.026 0.001 PHE A 94 TRP 0.010 0.001 TRP E 131 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00200 (10924) covalent geometry : angle 0.51106 (14819) hydrogen bonds : bond 0.02639 ( 673) hydrogen bonds : angle 3.07096 ( 1977) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.6792 (tmm) cc_final: 0.6141 (tmm) REVERT: A 90 MET cc_start: 0.8392 (tpp) cc_final: 0.8082 (tpp) REVERT: A 135 MET cc_start: 0.7141 (mmp) cc_final: 0.6832 (mmm) REVERT: C 40 LYS cc_start: 0.9017 (tttp) cc_final: 0.8762 (tttm) REVERT: D 23 LEU cc_start: 0.9336 (mt) cc_final: 0.9110 (tt) REVERT: D 490 MET cc_start: 0.9186 (tmm) cc_final: 0.8985 (tmm) REVERT: D 516 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8359 (pp) REVERT: F 49 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8549 (pp30) REVERT: F 153 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8577 (pp) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.0793 time to fit residues: 10.1530 Evaluate side-chains 74 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 109 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.067454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050820 restraints weight = 41816.113| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.99 r_work: 0.2820 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10924 Z= 0.096 Angle : 0.516 8.627 14819 Z= 0.246 Chirality : 0.037 0.190 1769 Planarity : 0.003 0.047 1850 Dihedral : 2.995 14.085 1477 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 16.88 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.24), residues: 1319 helix: 2.94 (0.19), residues: 802 sheet: -0.57 (0.50), residues: 91 loop : -0.83 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 90 TYR 0.010 0.001 TYR F 190 PHE 0.025 0.001 PHE A 94 TRP 0.015 0.001 TRP E 131 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00219 (10924) covalent geometry : angle 0.51593 (14819) hydrogen bonds : bond 0.02800 ( 673) hydrogen bonds : angle 3.06950 ( 1977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.26 seconds wall clock time: 42 minutes 16.01 seconds (2536.01 seconds total)