Starting phenix.real_space_refine on Mon Jul 28 21:48:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kau_22784/07_2025/7kau_22784.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kau_22784/07_2025/7kau_22784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kau_22784/07_2025/7kau_22784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kau_22784/07_2025/7kau_22784.map" model { file = "/net/cci-nas-00/data/ceres_data/7kau_22784/07_2025/7kau_22784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kau_22784/07_2025/7kau_22784.cif" } resolution = 4.0 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= 0.008 sd= 0.063 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 39 5.16 5 C 6981 2.51 5 N 1810 2.21 5 O 1881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10711 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3358 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 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: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 27, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 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: 6.33, per 1000 atoms: 0.59 Number of scatterers: 10711 At special positions: 0 Unit cell: (109.48, 127.33, 138.04, 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 39 16.00 O 1881 8.00 N 1810 7.00 C 6981 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: 3.46 Conformation dependent library (CDL) restraints added in 1.5 seconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 70.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.580A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 70 removed outlier: 3.658A pdb=" N ARG A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 107 through 137 removed outlier: 3.819A pdb=" N ARG A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.583A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.831A 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 213 through 225 removed outlier: 3.659A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.902A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.736A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 314 removed outlier: 4.114A pdb=" N ILE A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 346 removed outlier: 3.567A pdb=" N TYR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 346' Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 358 through 384 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.628A pdb=" N LYS A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 440 removed outlier: 3.630A pdb=" N GLY A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 466 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 4.219A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.517A pdb=" N VAL C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.524A pdb=" N PHE D 17 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 3.676A 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 67 removed outlier: 4.496A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 94 through 113 removed outlier: 3.548A pdb=" N ASN D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.572A pdb=" N GLY D 217 " --> pdb=" O PHE D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.907A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 249 removed outlier: 3.618A pdb=" N TYR D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.819A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.696A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.703A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.803A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 4.030A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.335A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.664A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.263A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 486 Processing helix chain 'D' and resid 487 through 492 removed outlier: 4.273A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.749A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 124 removed outlier: 4.006A pdb=" N LYS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.652A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 4.042A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.891A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.962A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.679A 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: 3.678A pdb=" N GLU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 4.045A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.762A pdb=" N LYS F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 removed outlier: 3.663A pdb=" N GLN F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.719A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 168 Processing helix chain 'F' and resid 175 through 192 Processing helix chain 'G' and resid 151 through 170 removed outlier: 3.598A 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: 3.511A pdb=" N GLU A 210 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 203 " --> pdb=" O GLU A 210 " (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 325 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 434 removed outlier: 6.842A pdb=" N LYS D 454 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA D 433 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N SER D 452 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.527A pdb=" N VAL D 590 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 604 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 592 " --> pdb=" O LEU D 602 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 602 " --> pdb=" O VAL D 592 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 678 hydrogen bonds defined for protein. 2004 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: 3.17 Time building geometry restraints manager: 3.52 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: 3390 1.34 - 1.46: 1852 1.46 - 1.57: 5615 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 10918 Sorted by residual: bond pdb=" C THR D 595 " pdb=" N ASP D 596 " ideal model delta sigma weight residual 1.332 1.316 0.016 1.40e-02 5.10e+03 1.34e+00 bond pdb=" C ILE D 425 " pdb=" N PRO D 426 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.11e-02 8.12e+03 9.83e-01 bond pdb=" CB TRP D 283 " pdb=" CG TRP D 283 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.78e-01 bond pdb=" CA GLN F 155 " pdb=" CB GLN F 155 " ideal model delta sigma weight residual 1.532 1.519 0.014 1.62e-02 3.81e+03 7.13e-01 bond pdb=" CA GLY A 176 " pdb=" C GLY A 176 " ideal model delta sigma weight residual 1.522 1.512 0.010 1.29e-02 6.01e+03 6.08e-01 ... (remaining 10913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 14637 1.99 - 3.99: 154 3.99 - 5.98: 15 5.98 - 7.98: 4 7.98 - 9.97: 1 Bond angle restraints: 14811 Sorted by residual: angle pdb=" N ILE E 126 " pdb=" CA ILE E 126 " pdb=" C ILE E 126 " ideal model delta sigma weight residual 113.71 109.99 3.72 9.50e-01 1.11e+00 1.53e+01 angle pdb=" N VAL E 205 " pdb=" CA VAL E 205 " pdb=" C VAL E 205 " ideal model delta sigma weight residual 111.88 108.56 3.32 1.06e+00 8.90e-01 9.80e+00 angle pdb=" CA VAL D 215 " pdb=" C VAL D 215 " pdb=" N ASP D 216 " ideal model delta sigma weight residual 116.60 120.55 -3.95 1.45e+00 4.76e-01 7.40e+00 angle pdb=" C GLU A 266 " pdb=" N LEU A 267 " pdb=" CA LEU A 267 " ideal model delta sigma weight residual 121.95 111.98 9.97 3.74e+00 7.15e-02 7.11e+00 angle pdb=" N SER A 289 " pdb=" CA SER A 289 " pdb=" C SER A 289 " ideal model delta sigma weight residual 111.11 114.24 -3.13 1.20e+00 6.94e-01 6.81e+00 ... (remaining 14806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 6066 17.36 - 34.72: 430 34.72 - 52.09: 62 52.09 - 69.45: 7 69.45 - 86.81: 8 Dihedral angle restraints: 6573 sinusoidal: 2514 harmonic: 4059 Sorted by residual: dihedral pdb=" CA VAL D 437 " pdb=" C VAL D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ILE D 425 " pdb=" C ILE D 425 " pdb=" N PRO D 426 " pdb=" CA PRO D 426 " ideal model delta harmonic sigma weight residual -180.00 -164.11 -15.89 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CB GLU D 473 " pdb=" CG GLU D 473 " pdb=" CD GLU D 473 " pdb=" OE1 GLU D 473 " ideal model delta sinusoidal sigma weight residual 0.00 -86.81 86.81 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 6570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 945 0.025 - 0.050: 540 0.050 - 0.076: 169 0.076 - 0.101: 73 0.101 - 0.126: 41 Chirality restraints: 1768 Sorted by residual: chirality pdb=" CA ILE D 470 " pdb=" N ILE D 470 " pdb=" C ILE D 470 " pdb=" CB ILE D 470 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PRO D 375 " pdb=" N PRO D 375 " pdb=" C PRO D 375 " pdb=" CB PRO D 375 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA THR A 291 " pdb=" N THR A 291 " pdb=" C THR A 291 " pdb=" CB THR A 291 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1765 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO F 48 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO F 94 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 437 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO D 438 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 438 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 438 " -0.019 5.00e-02 4.00e+02 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2401 2.78 - 3.31: 10631 3.31 - 3.84: 16840 3.84 - 4.37: 17505 4.37 - 4.90: 31497 Nonbonded interactions: 78874 Sorted by model distance: nonbonded pdb=" OD1 ASP D 308 " pdb=" NH1 ARG D 313 " model vdw 2.251 3.120 nonbonded pdb=" OG SER A 271 " pdb=" O VAL A 274 " model vdw 2.259 3.040 nonbonded pdb=" NZ LYS D 538 " pdb=" O ASP D 565 " model vdw 2.263 3.120 nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 66 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLN D 370 " pdb=" OG1 THR D 391 " model vdw 2.283 3.040 ... (remaining 78869 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 27.620 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 0.027 10918 Z= 0.151 Angle : 0.559 9.970 14811 Z= 0.311 Chirality : 0.038 0.126 1768 Planarity : 0.003 0.045 1846 Dihedral : 12.117 86.810 3935 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1316 helix: 0.39 (0.17), residues: 808 sheet: -2.21 (0.48), residues: 82 loop : -2.18 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 380 HIS 0.003 0.001 HIS B 72 PHE 0.015 0.001 PHE A 194 TYR 0.018 0.001 TYR F 190 ARG 0.002 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.12394 ( 678) hydrogen bonds : angle 4.49046 ( 2004) covalent geometry : bond 0.00319 (10918) covalent geometry : angle 0.55929 (14811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9095 (mmm) cc_final: 0.8823 (mmm) REVERT: A 290 ASN cc_start: 0.8938 (m-40) cc_final: 0.8511 (p0) REVERT: A 368 PHE cc_start: 0.9524 (t80) cc_final: 0.9241 (t80) REVERT: D 102 LEU cc_start: 0.8862 (mm) cc_final: 0.8460 (mm) REVERT: D 491 MET cc_start: 0.8811 (ttp) cc_final: 0.8126 (tmm) REVERT: D 601 ASP cc_start: 0.9055 (m-30) cc_final: 0.8821 (m-30) REVERT: E 81 MET cc_start: 0.8743 (ttm) cc_final: 0.8095 (tmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2433 time to fit residues: 37.9558 Evaluate side-chains 59 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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: 6.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 HIS D 494 GLN D 558 HIS E 88 HIS E 123 ASN E 174 GLN F 68 ASN F 70 GLN F 71 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.063166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.047345 restraints weight = 61624.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048593 restraints weight = 33490.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.049412 restraints weight = 23015.768| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10918 Z= 0.251 Angle : 0.645 7.998 14811 Z= 0.326 Chirality : 0.041 0.157 1768 Planarity : 0.004 0.047 1846 Dihedral : 3.781 20.692 1476 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.80 % Allowed : 12.58 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.24), residues: 1316 helix: 1.64 (0.18), residues: 810 sheet: -1.59 (0.50), residues: 78 loop : -1.73 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 380 HIS 0.005 0.001 HIS C 72 PHE 0.014 0.001 PHE D 547 TYR 0.023 0.002 TYR F 190 ARG 0.005 0.001 ARG D 440 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 678) hydrogen bonds : angle 4.05400 ( 2004) covalent geometry : bond 0.00566 (10918) covalent geometry : angle 0.64516 (14811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.9027 (t70) cc_final: 0.8735 (t0) REVERT: A 249 MET cc_start: 0.9156 (mmm) cc_final: 0.8917 (mmm) REVERT: A 290 ASN cc_start: 0.9025 (m-40) cc_final: 0.8617 (p0) REVERT: A 368 PHE cc_start: 0.9506 (t80) cc_final: 0.9297 (t80) REVERT: B 72 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.7709 (m170) REVERT: D 102 LEU cc_start: 0.8941 (mm) cc_final: 0.8555 (mm) REVERT: E 81 MET cc_start: 0.8629 (ttm) cc_final: 0.8115 (tmm) outliers start: 20 outliers final: 12 residues processed: 78 average time/residue: 0.1830 time to fit residues: 22.7706 Evaluate side-chains 69 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain E residue 170 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 7 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 100 optimal weight: 0.0370 chunk 48 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 87 optimal weight: 0.0970 overall best weight: 2.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 HIS D 381 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.063080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.048189 restraints weight = 60203.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049475 restraints weight = 31854.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050330 restraints weight = 21395.360| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10918 Z= 0.129 Angle : 0.514 6.917 14811 Z= 0.256 Chirality : 0.038 0.156 1768 Planarity : 0.003 0.046 1846 Dihedral : 3.532 21.194 1476 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.62 % Allowed : 15.09 % Favored : 83.29 % 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: 1.39 (0.24), residues: 1316 helix: 2.27 (0.19), residues: 816 sheet: -1.00 (0.53), residues: 82 loop : -1.48 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 380 HIS 0.004 0.001 HIS D 309 PHE 0.010 0.001 PHE D 547 TYR 0.016 0.001 TYR F 190 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 678) hydrogen bonds : angle 3.59694 ( 2004) covalent geometry : bond 0.00289 (10918) covalent geometry : angle 0.51378 (14811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.9045 (t70) cc_final: 0.8796 (t0) REVERT: A 249 MET cc_start: 0.9125 (mmm) cc_final: 0.8812 (mmm) REVERT: A 290 ASN cc_start: 0.9064 (m-40) cc_final: 0.8662 (p0) REVERT: B 72 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.7939 (m170) REVERT: D 102 LEU cc_start: 0.8989 (mm) cc_final: 0.8585 (mm) REVERT: D 608 MET cc_start: 0.8374 (ptt) cc_final: 0.7585 (ppp) REVERT: E 81 MET cc_start: 0.8828 (ttm) cc_final: 0.8278 (tmm) outliers start: 18 outliers final: 12 residues processed: 75 average time/residue: 0.1821 time to fit residues: 22.4125 Evaluate side-chains 65 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 62 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.063946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048586 restraints weight = 61309.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.049859 restraints weight = 32683.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050717 restraints weight = 22006.393| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10918 Z= 0.127 Angle : 0.513 7.858 14811 Z= 0.255 Chirality : 0.038 0.145 1768 Planarity : 0.003 0.044 1846 Dihedral : 3.421 20.877 1476 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.25 % Allowed : 15.81 % Favored : 81.94 % 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: 1.79 (0.24), residues: 1316 helix: 2.54 (0.18), residues: 818 sheet: -0.67 (0.56), residues: 82 loop : -1.28 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 380 HIS 0.004 0.001 HIS D 309 PHE 0.009 0.001 PHE D 547 TYR 0.016 0.001 TYR F 190 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 678) hydrogen bonds : angle 3.47193 ( 2004) covalent geometry : bond 0.00285 (10918) covalent geometry : angle 0.51319 (14811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9263 (mmm) cc_final: 0.8926 (mmm) REVERT: A 290 ASN cc_start: 0.9086 (m-40) cc_final: 0.8731 (p0) REVERT: B 72 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.7922 (m170) REVERT: D 102 LEU cc_start: 0.8940 (mm) cc_final: 0.8549 (mm) REVERT: D 608 MET cc_start: 0.8514 (ptt) cc_final: 0.7748 (ppp) REVERT: E 81 MET cc_start: 0.9019 (ttm) cc_final: 0.8430 (tmm) outliers start: 25 outliers final: 15 residues processed: 78 average time/residue: 0.1673 time to fit residues: 21.3453 Evaluate side-chains 70 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 87 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 0.0770 chunk 32 optimal weight: 6.9990 chunk 133 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 308 GLN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.062925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.047269 restraints weight = 61390.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048511 restraints weight = 33710.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.049316 restraints weight = 23119.757| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10918 Z= 0.217 Angle : 0.604 8.220 14811 Z= 0.300 Chirality : 0.040 0.149 1768 Planarity : 0.004 0.047 1846 Dihedral : 3.641 21.300 1476 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.70 % Allowed : 16.80 % Favored : 80.50 % 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: 1.75 (0.24), residues: 1316 helix: 2.47 (0.18), residues: 819 sheet: -0.67 (0.56), residues: 82 loop : -1.21 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 380 HIS 0.003 0.001 HIS C 72 PHE 0.013 0.001 PHE D 547 TYR 0.023 0.002 TYR F 190 ARG 0.003 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 678) hydrogen bonds : angle 3.76105 ( 2004) covalent geometry : bond 0.00490 (10918) covalent geometry : angle 0.60447 (14811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7774 (tp40) REVERT: A 237 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.5457 (m-10) REVERT: A 249 MET cc_start: 0.9196 (mmm) cc_final: 0.8912 (mmm) REVERT: A 290 ASN cc_start: 0.9118 (m-40) cc_final: 0.8759 (p0) REVERT: B 72 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8006 (m170) REVERT: D 102 LEU cc_start: 0.8995 (mm) cc_final: 0.8600 (mm) REVERT: D 526 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8388 (pp) REVERT: D 608 MET cc_start: 0.8437 (ptt) cc_final: 0.7705 (ppp) REVERT: E 81 MET cc_start: 0.8842 (ttm) cc_final: 0.8318 (tmm) outliers start: 30 outliers final: 21 residues processed: 77 average time/residue: 0.1664 time to fit residues: 21.5054 Evaluate side-chains 76 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 101 optimal weight: 0.0070 chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN D 334 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.059613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.044297 restraints weight = 59405.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045502 restraints weight = 33135.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.046305 restraints weight = 22856.628| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10918 Z= 0.103 Angle : 0.518 8.686 14811 Z= 0.253 Chirality : 0.037 0.129 1768 Planarity : 0.003 0.046 1846 Dihedral : 3.401 20.575 1476 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.52 % Allowed : 17.34 % Favored : 80.14 % 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: 2.05 (0.25), residues: 1316 helix: 2.64 (0.19), residues: 824 sheet: -0.26 (0.58), residues: 82 loop : -1.07 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 14 HIS 0.004 0.001 HIS D 309 PHE 0.008 0.001 PHE A 114 TYR 0.015 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 678) hydrogen bonds : angle 3.37347 ( 2004) covalent geometry : bond 0.00224 (10918) covalent geometry : angle 0.51832 (14811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7585 (tp40) REVERT: A 237 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5353 (m-10) REVERT: A 249 MET cc_start: 0.9116 (mmm) cc_final: 0.8806 (mmm) REVERT: A 290 ASN cc_start: 0.9018 (m-40) cc_final: 0.8657 (p0) REVERT: B 72 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8053 (m170) REVERT: D 102 LEU cc_start: 0.8965 (mm) cc_final: 0.8561 (mm) REVERT: D 608 MET cc_start: 0.8365 (ptt) cc_final: 0.7716 (ppp) REVERT: E 81 MET cc_start: 0.8755 (ttm) cc_final: 0.8249 (tmm) outliers start: 28 outliers final: 18 residues processed: 84 average time/residue: 0.1704 time to fit residues: 23.7323 Evaluate side-chains 79 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 94 optimal weight: 0.0060 chunk 60 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.058904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.043359 restraints weight = 60608.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.044571 restraints weight = 33607.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.045378 restraints weight = 23164.687| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10918 Z= 0.185 Angle : 0.575 8.948 14811 Z= 0.282 Chirality : 0.039 0.144 1768 Planarity : 0.003 0.047 1846 Dihedral : 3.527 20.876 1476 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.23 % Allowed : 17.79 % Favored : 78.98 % 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: 1.98 (0.24), residues: 1316 helix: 2.55 (0.19), residues: 825 sheet: -0.27 (0.62), residues: 72 loop : -1.01 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 380 HIS 0.003 0.001 HIS B 72 PHE 0.011 0.001 PHE D 547 TYR 0.021 0.001 TYR F 190 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 678) hydrogen bonds : angle 3.61614 ( 2004) covalent geometry : bond 0.00425 (10918) covalent geometry : angle 0.57513 (14811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7529 (tp40) REVERT: A 237 TYR cc_start: 0.5996 (OUTLIER) cc_final: 0.5471 (m-10) REVERT: A 249 MET cc_start: 0.9171 (mmm) cc_final: 0.8789 (mmm) REVERT: A 290 ASN cc_start: 0.9099 (m-40) cc_final: 0.8750 (p0) REVERT: B 72 HIS cc_start: 0.8758 (OUTLIER) cc_final: 0.8108 (m170) REVERT: D 102 LEU cc_start: 0.8999 (mm) cc_final: 0.8602 (mm) REVERT: D 370 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8869 (mt0) REVERT: D 526 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8480 (pp) REVERT: D 608 MET cc_start: 0.8419 (ptt) cc_final: 0.7648 (ppp) REVERT: E 81 MET cc_start: 0.8876 (ttm) cc_final: 0.8350 (tmm) outliers start: 36 outliers final: 26 residues processed: 87 average time/residue: 0.1648 time to fit residues: 23.5995 Evaluate side-chains 83 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 90 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 132 optimal weight: 30.0000 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 29 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 HIS E 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.060101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.044720 restraints weight = 59496.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.045981 restraints weight = 32450.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.046825 restraints weight = 22140.357| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10918 Z= 0.104 Angle : 0.537 10.391 14811 Z= 0.257 Chirality : 0.038 0.140 1768 Planarity : 0.003 0.047 1846 Dihedral : 3.353 20.062 1476 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.34 % Allowed : 18.60 % Favored : 79.07 % 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: 2.14 (0.24), residues: 1316 helix: 2.64 (0.19), residues: 825 sheet: -0.04 (0.63), residues: 72 loop : -0.91 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.004 0.001 HIS D 309 PHE 0.007 0.001 PHE D 294 TYR 0.015 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 678) hydrogen bonds : angle 3.34507 ( 2004) covalent geometry : bond 0.00233 (10918) covalent geometry : angle 0.53667 (14811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.6005 (OUTLIER) cc_final: 0.5479 (m-10) REVERT: A 249 MET cc_start: 0.9090 (mmm) cc_final: 0.8777 (mmm) REVERT: A 290 ASN cc_start: 0.9052 (m-40) cc_final: 0.8710 (p0) REVERT: B 72 HIS cc_start: 0.8701 (OUTLIER) cc_final: 0.8104 (m170) REVERT: D 102 LEU cc_start: 0.8978 (mm) cc_final: 0.8589 (mm) REVERT: D 526 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8423 (pp) REVERT: D 608 MET cc_start: 0.8323 (ptt) cc_final: 0.7660 (ppp) REVERT: E 81 MET cc_start: 0.8799 (ttm) cc_final: 0.8275 (tmm) outliers start: 26 outliers final: 19 residues processed: 80 average time/residue: 0.1778 time to fit residues: 23.5045 Evaluate side-chains 80 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.0970 chunk 30 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.058514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.043075 restraints weight = 59689.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.044251 restraints weight = 33326.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.045042 restraints weight = 23067.027| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10918 Z= 0.209 Angle : 0.607 10.417 14811 Z= 0.297 Chirality : 0.040 0.139 1768 Planarity : 0.003 0.047 1846 Dihedral : 3.563 20.678 1476 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.79 % Allowed : 18.51 % Favored : 78.71 % 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: 2.01 (0.24), residues: 1316 helix: 2.51 (0.18), residues: 827 sheet: -0.22 (0.62), residues: 72 loop : -0.87 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 156 HIS 0.003 0.001 HIS C 72 PHE 0.012 0.001 PHE D 547 TYR 0.022 0.001 TYR F 190 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 678) hydrogen bonds : angle 3.65737 ( 2004) covalent geometry : bond 0.00477 (10918) covalent geometry : angle 0.60710 (14811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.5615 (m-10) REVERT: A 249 MET cc_start: 0.9165 (mmm) cc_final: 0.8870 (mmm) REVERT: A 290 ASN cc_start: 0.9097 (m-40) cc_final: 0.8756 (p0) REVERT: B 72 HIS cc_start: 0.8780 (OUTLIER) cc_final: 0.8084 (m170) REVERT: D 102 LEU cc_start: 0.9022 (mm) cc_final: 0.8646 (mm) REVERT: D 526 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8489 (pp) REVERT: D 608 MET cc_start: 0.8414 (ptt) cc_final: 0.7695 (ppp) REVERT: E 81 MET cc_start: 0.8858 (ttm) cc_final: 0.8327 (tmm) outliers start: 31 outliers final: 26 residues processed: 81 average time/residue: 0.1727 time to fit residues: 23.1205 Evaluate side-chains 81 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 90 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.060469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045282 restraints weight = 58233.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.046562 restraints weight = 31542.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047403 restraints weight = 21348.400| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10918 Z= 0.099 Angle : 0.543 12.073 14811 Z= 0.259 Chirality : 0.037 0.134 1768 Planarity : 0.003 0.047 1846 Dihedral : 3.318 19.366 1476 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.43 % Allowed : 18.87 % Favored : 78.71 % 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: 2.22 (0.24), residues: 1316 helix: 2.68 (0.18), residues: 825 sheet: 0.06 (0.63), residues: 72 loop : -0.82 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 35 HIS 0.005 0.001 HIS D 309 PHE 0.008 0.001 PHE A 92 TYR 0.014 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 678) hydrogen bonds : angle 3.28600 ( 2004) covalent geometry : bond 0.00214 (10918) covalent geometry : angle 0.54306 (14811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9348 (tt) cc_final: 0.9071 (tp) REVERT: A 237 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5494 (m-10) REVERT: A 249 MET cc_start: 0.9068 (mmm) cc_final: 0.8747 (mmm) REVERT: A 290 ASN cc_start: 0.9118 (m-40) cc_final: 0.8702 (p0) REVERT: B 72 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8079 (m170) REVERT: D 102 LEU cc_start: 0.8990 (mm) cc_final: 0.8612 (mm) REVERT: D 526 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8410 (pp) REVERT: D 608 MET cc_start: 0.8324 (ptt) cc_final: 0.7684 (ppp) REVERT: E 81 MET cc_start: 0.8766 (ttm) cc_final: 0.8252 (tmm) outliers start: 27 outliers final: 21 residues processed: 85 average time/residue: 0.1725 time to fit residues: 24.2924 Evaluate side-chains 81 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 76 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 134 optimal weight: 50.0000 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 0.0020 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 HIS D 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.059789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.044454 restraints weight = 57836.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.045698 restraints weight = 31788.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.046416 restraints weight = 21778.474| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10918 Z= 0.135 Angle : 0.564 12.114 14811 Z= 0.272 Chirality : 0.038 0.159 1768 Planarity : 0.003 0.046 1846 Dihedral : 3.338 19.665 1476 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.70 % Allowed : 18.69 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.22 (0.24), residues: 1316 helix: 2.66 (0.19), residues: 825 sheet: 0.13 (0.62), residues: 72 loop : -0.80 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 380 HIS 0.003 0.001 HIS F 122 PHE 0.009 0.001 PHE D 547 TYR 0.018 0.001 TYR F 190 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 678) hydrogen bonds : angle 3.38704 ( 2004) covalent geometry : bond 0.00308 (10918) covalent geometry : angle 0.56364 (14811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3362.86 seconds wall clock time: 60 minutes 30.73 seconds (3630.73 seconds total)