Starting phenix.real_space_refine on Fri Feb 14 21:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kai_22771/02_2025/7kai_22771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kai_22771/02_2025/7kai_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_22771/02_2025/7kai_22771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kai_22771/02_2025/7kai_22771.map" model { file = "/net/cci-nas-00/data/ceres_data/7kai_22771/02_2025/7kai_22771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kai_22771/02_2025/7kai_22771.cif" } resolution = 3.2 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= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'PHE:plan': 1, 'ASP: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: {'GLN:plan1': 2, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 8} 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: {'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 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: 6.53, per 1000 atoms: 0.61 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: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.00 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: 3.30 Time building geometry restraints manager: 3.25 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: 0.730 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.050 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- 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= 0.188 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 (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: -1.28 (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 TRP 0.010 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 PHE 0.016 0.001 PHE D 547 TYR 0.012 0.001 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) ************************************************ 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 : 1.170 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2501 time to fit residues: 31.1170 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 : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 0.0070 chunk 55 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.067532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.050571 restraints weight = 40749.748| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.98 r_work: 0.2805 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10924 Z= 0.173 Angle : 0.509 11.864 14819 Z= 0.249 Chirality : 0.038 0.170 1769 Planarity : 0.004 0.048 1850 Dihedral : 3.259 16.698 1477 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.45 % Allowed : 8.53 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1319 helix: 1.61 (0.19), residues: 799 sheet: -2.10 (0.46), residues: 89 loop : -1.85 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 380 HIS 0.005 0.001 HIS D 330 PHE 0.023 0.001 PHE A 94 TYR 0.011 0.001 TYR F 190 ARG 0.004 0.000 ARG F 110 *********************** 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 : 1.281 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8330 (tpp) cc_final: 0.7476 (tpp) REVERT: A 94 PHE cc_start: 0.9381 (t80) cc_final: 0.8989 (m-10) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.2017 time to fit residues: 21.5196 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 : 1.190 ------------------------------------------------------------------------------- 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 122 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.067207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.050374 restraints weight = 41758.061| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.99 r_work: 0.2801 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10924 Z= 0.172 Angle : 0.493 10.827 14819 Z= 0.241 Chirality : 0.038 0.134 1769 Planarity : 0.003 0.047 1850 Dihedral : 3.172 16.185 1477 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.99 % Allowed : 9.87 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1319 helix: 2.13 (0.19), residues: 799 sheet: -1.75 (0.47), residues: 91 loop : -1.54 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 380 HIS 0.005 0.001 HIS D 330 PHE 0.016 0.001 PHE A 94 TYR 0.010 0.001 TYR F 190 ARG 0.002 0.000 ARG F 110 *********************** 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 77 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8350 (tpp) cc_final: 0.7665 (tpp) REVERT: A 94 PHE cc_start: 0.9409 (t80) cc_final: 0.9074 (m-80) REVERT: C 46 GLU cc_start: 0.8644 (tp30) cc_final: 0.8306 (tp30) REVERT: E 74 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8184 (tt) outliers start: 11 outliers final: 4 residues processed: 73 average time/residue: 0.1851 time to fit residues: 21.7467 Evaluate side-chains 64 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 112 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.065981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.049026 restraints weight = 41405.097| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.00 r_work: 0.2759 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10924 Z= 0.252 Angle : 0.527 10.868 14819 Z= 0.259 Chirality : 0.039 0.135 1769 Planarity : 0.003 0.048 1850 Dihedral : 3.266 16.834 1477 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.08 % Allowed : 11.49 % Favored : 87.43 % 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: 1.34 (0.24), residues: 1319 helix: 2.32 (0.19), residues: 801 sheet: -1.48 (0.48), residues: 91 loop : -1.45 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 PHE 0.013 0.001 PHE A 94 TYR 0.013 0.001 TYR F 190 ARG 0.003 0.000 ARG D 313 *********************** 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 73 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8439 (tpp) cc_final: 0.7755 (tpp) REVERT: A 94 PHE cc_start: 0.9423 (t80) cc_final: 0.9066 (m-80) REVERT: A 135 MET cc_start: 0.7279 (mmp) cc_final: 0.6987 (mmm) REVERT: A 350 MET cc_start: 0.8697 (mmm) cc_final: 0.8232 (mmm) REVERT: C 46 GLU cc_start: 0.8693 (tp30) cc_final: 0.8339 (tp30) REVERT: D 516 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8908 (pp) REVERT: E 74 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8171 (tt) REVERT: F 49 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8503 (pp30) REVERT: F 153 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8794 (pp) outliers start: 12 outliers final: 5 residues processed: 69 average time/residue: 0.1956 time to fit residues: 21.4344 Evaluate side-chains 68 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 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 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 78 optimal weight: 5.9990 chunk 108 optimal weight: 0.0770 chunk 136 optimal weight: 50.0000 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.065982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048998 restraints weight = 41362.847| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.99 r_work: 0.2761 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1474 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= 0.224 Angle : 0.511 10.407 14819 Z= 0.251 Chirality : 0.038 0.133 1769 Planarity : 0.003 0.049 1850 Dihedral : 3.242 16.570 1477 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.26 % Allowed : 12.75 % Favored : 86.00 % 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: 1.54 (0.24), residues: 1319 helix: 2.46 (0.19), residues: 801 sheet: -1.25 (0.48), residues: 91 loop : -1.35 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 PHE 0.011 0.001 PHE A 94 TYR 0.012 0.001 TYR F 190 ARG 0.002 0.000 ARG D 313 *********************** 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: 14 poor density : 62 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8447 (tpp) cc_final: 0.8158 (tpp) REVERT: A 135 MET cc_start: 0.7303 (mmp) cc_final: 0.6985 (mmm) REVERT: C 46 GLU cc_start: 0.8715 (tp30) cc_final: 0.8322 (tp30) REVERT: E 74 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8168 (tt) REVERT: F 153 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8744 (pp) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.1968 time to fit residues: 22.5878 Evaluate side-chains 69 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 71 ILE 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 E residue 74 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 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 93 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 132 optimal weight: 50.0000 chunk 79 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.065768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048820 restraints weight = 40771.402| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.01 r_work: 0.2781 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1590 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= 0.162 Angle : 0.496 9.677 14819 Z= 0.241 Chirality : 0.037 0.132 1769 Planarity : 0.003 0.048 1850 Dihedral : 3.145 15.636 1477 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.08 % Allowed : 14.18 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1319 helix: 2.61 (0.19), residues: 802 sheet: -1.09 (0.49), residues: 91 loop : -1.25 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 131 HIS 0.005 0.001 HIS D 330 PHE 0.008 0.001 PHE D 481 TYR 0.011 0.001 TYR F 190 ARG 0.002 0.000 ARG D 313 *********************** 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: 12 poor density : 64 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8443 (tpp) cc_final: 0.8144 (tpp) REVERT: C 46 GLU cc_start: 0.8722 (tp30) cc_final: 0.8316 (tp30) REVERT: D 516 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8764 (pp) REVERT: E 74 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8138 (tt) REVERT: F 153 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8696 (pp) outliers start: 12 outliers final: 5 residues processed: 73 average time/residue: 0.1855 time to fit residues: 21.8948 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 : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 40 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 0.0770 chunk 75 optimal weight: 0.3980 chunk 135 optimal weight: 50.0000 overall best weight: 2.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.048297 restraints weight = 42262.018| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.00 r_work: 0.2741 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10924 Z= 0.286 Angle : 0.564 10.281 14819 Z= 0.277 Chirality : 0.039 0.154 1769 Planarity : 0.004 0.048 1850 Dihedral : 3.325 17.269 1477 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.26 % Allowed : 14.54 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1319 helix: 2.58 (0.19), residues: 802 sheet: -0.99 (0.50), residues: 91 loop : -1.23 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 PHE 0.010 0.001 PHE A 424 TYR 0.014 0.001 TYR F 190 ARG 0.003 0.000 ARG D 313 *********************** 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 75 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8438 (tpp) cc_final: 0.8147 (tpp) REVERT: A 135 MET cc_start: 0.7292 (mmp) cc_final: 0.7031 (mmm) REVERT: D 516 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8923 (pp) REVERT: F 153 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8820 (pp) outliers start: 14 outliers final: 8 residues processed: 73 average time/residue: 0.1922 time to fit residues: 22.5371 Evaluate side-chains 68 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 424 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.065835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.049004 restraints weight = 41267.074| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.96 r_work: 0.2764 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10924 Z= 0.207 Angle : 0.535 9.726 14819 Z= 0.261 Chirality : 0.038 0.133 1769 Planarity : 0.003 0.049 1850 Dihedral : 3.256 16.261 1477 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.90 % Allowed : 15.35 % Favored : 83.75 % 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: 1.87 (0.24), residues: 1319 helix: 2.67 (0.19), residues: 800 sheet: -0.89 (0.49), residues: 91 loop : -1.16 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 PHE 0.010 0.001 PHE D 481 TYR 0.012 0.001 TYR F 190 ARG 0.002 0.000 ARG D 313 *********************** 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 73 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8443 (tpp) cc_final: 0.8139 (tpp) REVERT: A 135 MET cc_start: 0.7261 (mmp) cc_final: 0.6982 (mmm) REVERT: D 516 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8885 (pp) REVERT: F 153 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8692 (pp) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.2039 time to fit residues: 22.4396 Evaluate side-chains 69 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain D residue 266 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 91 optimal weight: 6.9990 chunk 135 optimal weight: 50.0000 chunk 92 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.066092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.049274 restraints weight = 41631.294| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.98 r_work: 0.2771 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10924 Z= 0.196 Angle : 0.540 9.427 14819 Z= 0.261 Chirality : 0.038 0.134 1769 Planarity : 0.003 0.049 1850 Dihedral : 3.206 15.901 1477 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.90 % Allowed : 15.26 % Favored : 83.84 % 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: 1.95 (0.24), residues: 1319 helix: 2.72 (0.19), residues: 801 sheet: -0.80 (0.50), residues: 91 loop : -1.11 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 PHE 0.010 0.001 PHE D 481 TYR 0.012 0.001 TYR F 190 ARG 0.008 0.000 ARG F 90 *********************** 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 72 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8439 (tpp) cc_final: 0.8143 (tpp) REVERT: A 135 MET cc_start: 0.7264 (mmp) cc_final: 0.6968 (mmm) REVERT: D 516 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8806 (pp) REVERT: E 147 ASP cc_start: 0.9484 (t0) cc_final: 0.9257 (t0) REVERT: E 150 GLN cc_start: 0.8955 (pp30) cc_final: 0.8542 (pp30) REVERT: F 153 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8679 (pp) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.1968 time to fit residues: 22.3162 Evaluate side-chains 71 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain D residue 266 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 100 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 0.0270 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.067022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.050289 restraints weight = 41043.907| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.98 r_work: 0.2807 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10924 Z= 0.150 Angle : 0.513 8.790 14819 Z= 0.246 Chirality : 0.037 0.135 1769 Planarity : 0.003 0.049 1850 Dihedral : 3.065 14.357 1477 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.81 % Allowed : 15.26 % Favored : 83.93 % 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: 2.09 (0.24), residues: 1319 helix: 2.79 (0.19), residues: 806 sheet: -0.70 (0.50), residues: 91 loop : -1.02 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 131 HIS 0.005 0.001 HIS D 330 PHE 0.008 0.001 PHE E 163 TYR 0.009 0.001 TYR F 190 ARG 0.007 0.000 ARG F 90 ********************** 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 79 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8413 (tpp) cc_final: 0.8107 (tpp) REVERT: A 135 MET cc_start: 0.7208 (mmp) cc_final: 0.6892 (mmm) REVERT: C 40 LYS cc_start: 0.9114 (tttp) cc_final: 0.8856 (tttm) REVERT: D 23 LEU cc_start: 0.9357 (mt) cc_final: 0.9112 (tt) REVERT: D 516 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8441 (pp) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.1886 time to fit residues: 23.0112 Evaluate side-chains 72 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain D residue 266 LEU 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 129 ASP Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 129 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 85 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.066627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.049851 restraints weight = 41449.401| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.97 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: 0.8664 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10924 Z= 0.174 Angle : 0.527 8.843 14819 Z= 0.253 Chirality : 0.037 0.134 1769 Planarity : 0.003 0.048 1850 Dihedral : 3.070 14.938 1477 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.72 % Allowed : 15.62 % Favored : 83.66 % 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 (0.24), residues: 1319 helix: 2.84 (0.19), residues: 803 sheet: -0.66 (0.51), residues: 91 loop : -1.02 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 131 HIS 0.005 0.001 HIS D 330 PHE 0.009 0.001 PHE D 481 TYR 0.011 0.001 TYR F 190 ARG 0.007 0.000 ARG F 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4922.15 seconds wall clock time: 87 minutes 57.57 seconds (5277.57 seconds total)