Starting phenix.real_space_refine on Fri Jul 3 00:39:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c80_16467/07_2026/8c80_16467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c80_16467/07_2026/8c80_16467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8c80_16467/07_2026/8c80_16467.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c80_16467/07_2026/8c80_16467.cif" model { file = "/net/cci-nas-00/data/ceres_data/8c80_16467/07_2026/8c80_16467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c80_16467/07_2026/8c80_16467.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c80_16467/07_2026/8c80_16467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c80_16467/07_2026/8c80_16467.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 55 5.16 5 C 7088 2.51 5 N 1795 2.21 5 O 2029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10968 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1502 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "B" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4214 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "C" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "D" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 626 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'ERG': 2, 'Z8A': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ERG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.34, per 1000 atoms: 0.21 Number of scatterers: 10968 At special positions: 0 Unit cell: (90.552, 108.108, 126.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 1 15.00 O 2029 8.00 N 1795 7.00 C 7088 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 413.6 milliseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2542 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 51.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 62 through 72 removed outlier: 4.072A pdb=" N LEU A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 removed outlier: 4.224A pdb=" N VAL A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 129 removed outlier: 3.632A pdb=" N LEU A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.547A pdb=" N ALA A 141 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.539A pdb=" N PHE A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 removed outlier: 4.178A pdb=" N LEU B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 53 through 73 removed outlier: 3.907A pdb=" N THR B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 3.521A pdb=" N TRP B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.536A pdb=" N TYR B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 217 through 226 Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 239 through 250 removed outlier: 4.067A pdb=" N ARG B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.817A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 4.015A pdb=" N LEU B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.511A pdb=" N HIS B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.868A pdb=" N ILE B 347 " --> pdb=" O ARG B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.576A pdb=" N CYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.726A pdb=" N VAL B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 426 Processing helix chain 'B' and resid 450 through 459 removed outlier: 3.725A pdb=" N SER B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 476 Processing helix chain 'B' and resid 482 through 503 Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 534 through 555 removed outlier: 3.537A pdb=" N CYS B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 57 through 86 removed outlier: 3.930A pdb=" N SER C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.914A pdb=" N LEU C 94 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 118 through 123 removed outlier: 4.289A pdb=" N PHE C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 123' Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.593A pdb=" N VAL C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.522A pdb=" N ILE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.596A pdb=" N PHE C 236 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.509A pdb=" N ARG C 254 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 removed outlier: 3.734A pdb=" N VAL C 284 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.570A pdb=" N GLU C 319 " --> pdb=" O PRO C 315 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.857A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 399 through 410 removed outlier: 3.733A pdb=" N LEU C 403 " --> pdb=" O PRO C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 464 through 476 removed outlier: 3.688A pdb=" N ALA C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET C 473 " --> pdb=" O PHE C 469 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C 475 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 476 " --> pdb=" O MET C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 488 Processing helix chain 'C' and resid 504 through 523 Processing helix chain 'C' and resid 541 through 553 Proline residue: C 550 - end of helix Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.993A pdb=" N LYS D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 removed outlier: 4.151A pdb=" N GLU D 33 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL D 34 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 41 " --> pdb=" O LYS D 37 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 76 removed outlier: 3.612A pdb=" N LEU D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.406A pdb=" N ILE B 133 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 142 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N LEU B 506 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE B 148 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.587A pdb=" N GLY B 367 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 316 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL B 231 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL B 289 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 233 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N GLU B 291 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ASP B 235 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 232 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE B 256 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA B 234 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 436 removed outlier: 3.558A pdb=" N ILE B 435 " --> pdb=" O GLN B 448 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 142 removed outlier: 3.523A pdb=" N CYS C 136 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 155 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 138 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ALA C 153 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ILE C 140 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER C 151 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N HIS C 142 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR C 149 " --> pdb=" O HIS C 142 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ALA C 479 " --> pdb=" O PRO C 156 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N MET C 158 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.536A pdb=" N ASP C 218 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY C 373 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE C 297 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N PHE C 329 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE C 299 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASP C 331 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 246 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 267 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.587A pdb=" N SER C 493 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL C 481 " --> pdb=" O ARG C 496 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2964 1.33 - 1.45: 2008 1.45 - 1.57: 6179 1.57 - 1.69: 4 1.69 - 1.81: 83 Bond restraints: 11238 Sorted by residual: bond pdb=" N ILE D 27 " pdb=" CA ILE D 27 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N ASN B 188 " pdb=" CA ASN B 188 " ideal model delta sigma weight residual 1.455 1.498 -0.044 1.27e-02 6.20e+03 1.18e+01 bond pdb=" N ASN A 144 " pdb=" CA ASN A 144 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.16e+01 bond pdb=" N GLN C 23 " pdb=" CA GLN C 23 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.32e-02 5.74e+03 1.13e+01 bond pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.31e-02 5.83e+03 9.76e+00 ... (remaining 11233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 14943 2.55 - 5.10: 284 5.10 - 7.65: 38 7.65 - 10.20: 6 10.20 - 12.76: 2 Bond angle restraints: 15273 Sorted by residual: angle pdb=" N LEU D 28 " pdb=" CA LEU D 28 " pdb=" C LEU D 28 " ideal model delta sigma weight residual 113.16 100.40 12.76 1.24e+00 6.50e-01 1.06e+02 angle pdb=" N THR A 194 " pdb=" CA THR A 194 " pdb=" C THR A 194 " ideal model delta sigma weight residual 110.97 120.01 -9.04 1.09e+00 8.42e-01 6.88e+01 angle pdb=" C ILE D 31 " pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta sigma weight residual 120.38 111.58 8.80 1.37e+00 5.33e-01 4.12e+01 angle pdb=" C THR D 30 " pdb=" N ILE D 31 " pdb=" CA ILE D 31 " ideal model delta sigma weight residual 122.66 116.60 6.06 9.70e-01 1.06e+00 3.90e+01 angle pdb=" N ILE D 31 " pdb=" CA ILE D 31 " pdb=" C ILE D 31 " ideal model delta sigma weight residual 111.90 107.04 4.86 8.10e-01 1.52e+00 3.60e+01 ... (remaining 15268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.51: 6592 27.51 - 55.01: 211 55.01 - 82.52: 29 82.52 - 110.03: 16 110.03 - 137.53: 12 Dihedral angle restraints: 6860 sinusoidal: 2910 harmonic: 3950 Sorted by residual: dihedral pdb=" C5A PLP C 601 " pdb=" O4P PLP C 601 " pdb=" P PLP C 601 " pdb=" O1P PLP C 601 " ideal model delta sinusoidal sigma weight residual 76.43 174.49 -98.06 1 2.00e+01 2.50e-03 2.74e+01 dihedral pdb=" C2B Q7G C 602 " pdb=" C1B Q7G C 602 " pdb=" O5B Q7G C 602 " pdb=" C5B Q7G C 602 " ideal model delta sinusoidal sigma weight residual -63.14 74.39 -137.53 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C5B Q7G C 602 " pdb=" C1B Q7G C 602 " pdb=" O5B Q7G C 602 " pdb=" O1B Q7G C 602 " ideal model delta sinusoidal sigma weight residual 301.16 167.13 134.03 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 6857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1508 0.072 - 0.143: 202 0.143 - 0.215: 14 0.215 - 0.286: 14 0.286 - 0.358: 2 Chirality restraints: 1740 Sorted by residual: chirality pdb=" CA LEU D 28 " pdb=" N LEU D 28 " pdb=" C LEU D 28 " pdb=" CB LEU D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C4 Z8A A 302 " pdb=" C3 Z8A A 302 " pdb=" C5 Z8A A 302 " pdb=" O2 Z8A A 302 " both_signs ideal model delta sigma weight residual False -2.29 -2.63 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C51 Q7G C 602 " pdb=" C41 Q7G C 602 " pdb=" C61 Q7G C 602 " pdb=" O51 Q7G C 602 " both_signs ideal model delta sigma weight residual False -2.21 -2.49 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1737 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 301 " -0.097 2.00e-02 2.50e+03 9.78e-02 9.56e+01 pdb=" C22 ERG A 301 " 0.096 2.00e-02 2.50e+03 pdb=" C23 ERG A 301 " 0.099 2.00e-02 2.50e+03 pdb=" C24 ERG A 301 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G C 602 " 0.018 2.00e-02 2.50e+03 6.86e-02 5.88e+01 pdb=" C13 Q7G C 602 " 0.011 2.00e-02 2.50e+03 pdb=" C14 Q7G C 602 " 0.113 2.00e-02 2.50e+03 pdb=" C15 Q7G C 602 " -0.083 2.00e-02 2.50e+03 pdb=" C16 Q7G C 602 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 303 " -0.052 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" C22 ERG A 303 " 0.052 2.00e-02 2.50e+03 pdb=" C23 ERG A 303 " 0.052 2.00e-02 2.50e+03 pdb=" C24 ERG A 303 " -0.052 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 46 2.56 - 3.15: 8566 3.15 - 3.73: 14955 3.73 - 4.32: 20247 4.32 - 4.90: 35209 Nonbonded interactions: 79023 Sorted by model distance: nonbonded pdb=" CD1 PHE B 185 " pdb=" CD1 TYR B 186 " model vdw 1.975 3.640 nonbonded pdb=" CD1 PHE B 185 " pdb=" N TYR B 186 " model vdw 2.182 3.420 nonbonded pdb=" OH TYR B 460 " pdb=" OE1 GLU B 488 " model vdw 2.215 3.040 nonbonded pdb=" O ALA B 183 " pdb=" ND2 ASN B 188 " model vdw 2.262 3.120 nonbonded pdb=" O ASN A 74 " pdb=" OG1 THR A 78 " model vdw 2.273 3.040 ... (remaining 79018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.006 0.055 11239 Z= 0.300 Angle : 0.848 12.756 15273 Z= 0.489 Chirality : 0.054 0.358 1740 Planarity : 0.006 0.098 1904 Dihedral : 15.686 137.534 4318 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.75 % Allowed : 5.02 % Favored : 94.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.20), residues: 1342 helix: -0.34 (0.19), residues: 595 sheet: 0.32 (0.51), residues: 113 loop : -1.86 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 454 TYR 0.028 0.002 TYR B 186 PHE 0.013 0.001 PHE C 109 TRP 0.009 0.001 TRP C 102 HIS 0.010 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.30 (11238) covalent geometry : angle 0.84761 / 0.49 (15273) hydrogen bonds : bond 0.28392 / 19.37 ( 466) hydrogen bonds : angle 7.74949 / 5.39 ( 1350) Misc. bond : bond 0.03814 / 2.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 233 time to evaluate : 0.412 Fit side-chains REVERT: A 82 GLN cc_start: 0.8846 (mm110) cc_final: 0.8629 (mm-40) REVERT: B 274 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7826 (tp-100) REVERT: B 373 LEU cc_start: 0.9189 (tp) cc_final: 0.8924 (tt) REVERT: B 547 GLN cc_start: 0.7333 (tp40) cc_final: 0.7081 (tm-30) REVERT: C 23 GLN cc_start: 0.8608 (tp40) cc_final: 0.8380 (tp40) REVERT: D 7 SER cc_start: 0.8750 (t) cc_final: 0.8382 (p) outliers start: 9 outliers final: 2 residues processed: 240 average time/residue: 0.1061 time to fit residues: 35.7162 Evaluate side-chains 114 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 220 GLN B 50 HIS C 90 HIS C 142 HIS C 145 ASN C 170 GLN C 229 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111047 restraints weight = 17567.012| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.69 r_work: 0.3405 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11239 Z= 0.132 Angle : 0.632 10.870 15273 Z= 0.311 Chirality : 0.045 0.306 1740 Planarity : 0.004 0.042 1904 Dihedral : 12.429 123.390 1743 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.76 % Allowed : 11.55 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1342 helix: 1.27 (0.21), residues: 609 sheet: 0.93 (0.49), residues: 116 loop : -1.68 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.021 0.001 TYR B 66 PHE 0.026 0.001 PHE C 106 TRP 0.014 0.001 TRP A 188 HIS 0.007 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (11238) covalent geometry : angle 0.63242 / 0.31 (15273) hydrogen bonds : bond 0.04770 / 3.20 ( 466) hydrogen bonds : angle 4.52284 / 3.12 ( 1350) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.369 Fit side-chains REVERT: A 143 ASP cc_start: 0.8517 (t0) cc_final: 0.8254 (t0) REVERT: A 207 ARG cc_start: 0.8775 (mtp85) cc_final: 0.8552 (mtt-85) REVERT: B 91 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7735 (mp10) REVERT: B 469 MET cc_start: 0.8281 (tpt) cc_final: 0.7872 (tpt) REVERT: D 7 SER cc_start: 0.8749 (t) cc_final: 0.8452 (p) REVERT: D 37 LYS cc_start: 0.7276 (tttm) cc_final: 0.6905 (tppt) outliers start: 21 outliers final: 7 residues processed: 146 average time/residue: 0.1001 time to fit residues: 20.7641 Evaluate side-chains 111 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 72 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN C 90 HIS C 229 ASN C 291 ASN D 60 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104049 restraints weight = 17982.269| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.68 r_work: 0.3302 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11239 Z= 0.152 Angle : 0.626 9.295 15273 Z= 0.312 Chirality : 0.044 0.256 1740 Planarity : 0.004 0.043 1904 Dihedral : 10.513 115.370 1740 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.76 % Allowed : 12.22 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.23), residues: 1342 helix: 1.67 (0.22), residues: 613 sheet: 0.87 (0.44), residues: 144 loop : -1.71 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 132 TYR 0.015 0.001 TYR C 510 PHE 0.020 0.001 PHE D 62 TRP 0.013 0.001 TRP A 188 HIS 0.007 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (11238) covalent geometry : angle 0.62643 / 0.31 (15273) hydrogen bonds : bond 0.06243 / 4.19 ( 466) hydrogen bonds : angle 4.20438 / 2.91 ( 1350) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8541 (t0) cc_final: 0.8326 (t0) REVERT: B 293 ILE cc_start: 0.8965 (mm) cc_final: 0.8663 (mm) REVERT: B 337 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: C 292 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7415 (mtp85) REVERT: C 405 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: C 424 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: D 7 SER cc_start: 0.8802 (t) cc_final: 0.8520 (p) REVERT: D 37 LYS cc_start: 0.7587 (tttm) cc_final: 0.7178 (tppt) outliers start: 33 outliers final: 22 residues processed: 141 average time/residue: 0.1028 time to fit residues: 20.7564 Evaluate side-chains 127 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 552 CYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN D 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102511 restraints weight = 17921.280| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.64 r_work: 0.3278 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11239 Z= 0.156 Angle : 0.591 9.873 15273 Z= 0.298 Chirality : 0.044 0.227 1740 Planarity : 0.004 0.043 1904 Dihedral : 9.932 125.121 1740 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.35 % Allowed : 12.72 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1342 helix: 1.82 (0.22), residues: 608 sheet: 0.64 (0.49), residues: 118 loop : -1.63 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 132 TYR 0.017 0.001 TYR C 510 PHE 0.015 0.001 PHE B 318 TRP 0.018 0.001 TRP A 188 HIS 0.004 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (11238) covalent geometry : angle 0.59053 / 0.30 (15273) hydrogen bonds : bond 0.05625 / 3.77 ( 466) hydrogen bonds : angle 4.13513 / 2.88 ( 1350) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.451 Fit side-chains REVERT: A 143 ASP cc_start: 0.8648 (t0) cc_final: 0.8439 (t0) REVERT: B 92 GLU cc_start: 0.8546 (mp0) cc_final: 0.8308 (mt-10) REVERT: B 377 ILE cc_start: 0.8619 (tp) cc_final: 0.8398 (tp) REVERT: C 78 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.8109 (m-70) REVERT: C 146 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: C 272 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7904 (mmt) REVERT: C 292 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7397 (mtp85) REVERT: C 405 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: D 5 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7046 (mmtp) REVERT: D 7 SER cc_start: 0.8806 (t) cc_final: 0.8466 (p) REVERT: D 37 LYS cc_start: 0.7714 (tttm) cc_final: 0.7382 (tppt) outliers start: 40 outliers final: 26 residues processed: 141 average time/residue: 0.0930 time to fit residues: 18.9476 Evaluate side-chains 133 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 552 CYS Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 128 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.125137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101749 restraints weight = 18045.133| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.69 r_work: 0.3271 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11239 Z= 0.148 Angle : 0.573 9.317 15273 Z= 0.291 Chirality : 0.043 0.224 1740 Planarity : 0.004 0.043 1904 Dihedral : 9.810 123.356 1740 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.26 % Allowed : 13.64 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.23), residues: 1342 helix: 1.87 (0.22), residues: 609 sheet: 0.68 (0.50), residues: 118 loop : -1.63 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 207 TYR 0.016 0.001 TYR C 510 PHE 0.014 0.001 PHE B 318 TRP 0.012 0.001 TRP A 110 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11238) covalent geometry : angle 0.57314 / 0.29 (15273) hydrogen bonds : bond 0.05566 / 3.73 ( 466) hydrogen bonds : angle 4.08964 / 2.84 ( 1350) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.260 Fit side-chains REVERT: A 143 ASP cc_start: 0.8706 (t0) cc_final: 0.8474 (t0) REVERT: B 92 GLU cc_start: 0.8546 (mp0) cc_final: 0.8346 (mt-10) REVERT: B 280 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8606 (tt) REVERT: B 293 ILE cc_start: 0.8936 (mm) cc_final: 0.8701 (mm) REVERT: B 533 MET cc_start: 0.8657 (mtt) cc_final: 0.8270 (mtt) REVERT: C 78 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8275 (m-70) REVERT: C 119 ASP cc_start: 0.9002 (t0) cc_final: 0.8555 (t0) REVERT: C 146 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8417 (mm-30) REVERT: C 272 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7832 (mmt) REVERT: C 292 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7358 (mtp85) REVERT: C 405 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8324 (tp40) REVERT: D 5 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7030 (mmtp) REVERT: D 37 LYS cc_start: 0.7833 (tttm) cc_final: 0.7487 (tppt) outliers start: 39 outliers final: 23 residues processed: 138 average time/residue: 0.0954 time to fit residues: 19.2300 Evaluate side-chains 132 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 8 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN A 138 ASN D 29 ASN D 60 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099884 restraints weight = 18117.671| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.68 r_work: 0.3240 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11239 Z= 0.173 Angle : 0.589 9.859 15273 Z= 0.302 Chirality : 0.044 0.214 1740 Planarity : 0.004 0.042 1904 Dihedral : 9.817 122.579 1740 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.01 % Allowed : 14.39 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1342 helix: 1.89 (0.22), residues: 603 sheet: 0.83 (0.48), residues: 120 loop : -1.71 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 132 TYR 0.017 0.001 TYR C 510 PHE 0.015 0.001 PHE B 318 TRP 0.013 0.001 TRP A 110 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (11238) covalent geometry : angle 0.58896 / 0.30 (15273) hydrogen bonds : bond 0.06153 / 4.12 ( 466) hydrogen bonds : angle 4.15626 / 2.88 ( 1350) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.410 Fit side-chains REVERT: A 143 ASP cc_start: 0.8741 (t0) cc_final: 0.8537 (t0) REVERT: B 92 GLU cc_start: 0.8578 (mp0) cc_final: 0.8368 (mt-10) REVERT: B 261 MET cc_start: 0.7544 (mmp) cc_final: 0.6785 (mmp) REVERT: B 280 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 293 ILE cc_start: 0.8955 (mm) cc_final: 0.8702 (mm) REVERT: B 424 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7192 (t80) REVERT: B 533 MET cc_start: 0.8686 (mtt) cc_final: 0.8286 (mtt) REVERT: C 17 GLU cc_start: 0.8535 (pm20) cc_final: 0.7616 (tm-30) REVERT: C 78 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8051 (m-70) REVERT: C 117 ARG cc_start: 0.8189 (mpt180) cc_final: 0.7631 (mmm-85) REVERT: C 119 ASP cc_start: 0.9135 (t0) cc_final: 0.8665 (t0) REVERT: C 146 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8341 (mt-10) REVERT: C 239 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8158 (ttpp) REVERT: C 272 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7961 (mmt) REVERT: C 292 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7364 (mtp85) REVERT: C 405 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8358 (tp40) REVERT: D 5 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7050 (mmtp) REVERT: D 37 LYS cc_start: 0.7975 (tttm) cc_final: 0.7595 (tppt) outliers start: 36 outliers final: 26 residues processed: 134 average time/residue: 0.0947 time to fit residues: 18.2936 Evaluate side-chains 135 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102520 restraints weight = 17595.146| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.32 r_work: 0.3210 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11239 Z= 0.126 Angle : 0.546 9.228 15273 Z= 0.277 Chirality : 0.042 0.213 1740 Planarity : 0.004 0.041 1904 Dihedral : 9.636 120.946 1740 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.68 % Allowed : 14.81 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1342 helix: 1.96 (0.22), residues: 608 sheet: 0.61 (0.50), residues: 118 loop : -1.63 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.017 0.001 TYR D 39 PHE 0.013 0.001 PHE C 329 TRP 0.013 0.001 TRP A 110 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (11238) covalent geometry : angle 0.54571 / 0.28 (15273) hydrogen bonds : bond 0.05094 / 3.41 ( 466) hydrogen bonds : angle 4.02915 / 2.80 ( 1350) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.373 Fit side-chains REVERT: B 261 MET cc_start: 0.7621 (mmp) cc_final: 0.6860 (mmp) REVERT: B 280 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8636 (tt) REVERT: B 293 ILE cc_start: 0.8997 (mm) cc_final: 0.8758 (mm) REVERT: B 533 MET cc_start: 0.8729 (mtt) cc_final: 0.8377 (mtt) REVERT: C 17 GLU cc_start: 0.8546 (pm20) cc_final: 0.7671 (tm-30) REVERT: C 78 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.8411 (m-70) REVERT: C 117 ARG cc_start: 0.8228 (mpt180) cc_final: 0.7714 (mmm-85) REVERT: C 119 ASP cc_start: 0.9233 (t0) cc_final: 0.8807 (t0) REVERT: C 146 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8483 (mt-10) REVERT: C 239 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8109 (ttpp) REVERT: C 292 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7608 (mtp85) REVERT: D 5 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7178 (mmtp) REVERT: D 37 LYS cc_start: 0.8210 (tttm) cc_final: 0.7797 (tppt) outliers start: 32 outliers final: 24 residues processed: 136 average time/residue: 0.0969 time to fit residues: 19.2141 Evaluate side-chains 133 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 0.0470 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.104071 restraints weight = 17655.274| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.33 r_work: 0.3237 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11239 Z= 0.106 Angle : 0.521 8.626 15273 Z= 0.263 Chirality : 0.041 0.223 1740 Planarity : 0.004 0.040 1904 Dihedral : 9.401 118.575 1740 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.34 % Allowed : 15.73 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1342 helix: 2.02 (0.22), residues: 613 sheet: 0.71 (0.51), residues: 116 loop : -1.60 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.015 0.001 TYR B 66 PHE 0.012 0.001 PHE C 329 TRP 0.012 0.001 TRP A 110 HIS 0.002 0.000 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11238) covalent geometry : angle 0.52077 / 0.26 (15273) hydrogen bonds : bond 0.04361 / 2.91 ( 466) hydrogen bonds : angle 3.93883 / 2.74 ( 1350) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.328 Fit side-chains REVERT: B 261 MET cc_start: 0.7583 (mmp) cc_final: 0.6786 (mmp) REVERT: B 280 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8589 (tt) REVERT: B 293 ILE cc_start: 0.8995 (mm) cc_final: 0.8727 (mm) REVERT: B 533 MET cc_start: 0.8727 (mtt) cc_final: 0.8359 (mtt) REVERT: C 117 ARG cc_start: 0.8176 (mpt180) cc_final: 0.7726 (mmm-85) REVERT: C 119 ASP cc_start: 0.9244 (t0) cc_final: 0.8846 (t0) REVERT: C 146 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8432 (mt-10) REVERT: C 272 MET cc_start: 0.8680 (mmp) cc_final: 0.8283 (mmp) REVERT: D 5 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7183 (mmtp) REVERT: D 37 LYS cc_start: 0.8089 (tttm) cc_final: 0.7687 (tppt) outliers start: 28 outliers final: 20 residues processed: 132 average time/residue: 0.0943 time to fit residues: 18.0024 Evaluate side-chains 127 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 192 HIS B 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101409 restraints weight = 17629.942| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.33 r_work: 0.3178 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11239 Z= 0.142 Angle : 0.558 9.062 15273 Z= 0.284 Chirality : 0.042 0.219 1740 Planarity : 0.004 0.041 1904 Dihedral : 9.424 117.574 1740 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.26 % Allowed : 15.98 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1342 helix: 2.02 (0.22), residues: 609 sheet: 0.60 (0.51), residues: 118 loop : -1.60 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 207 TYR 0.017 0.001 TYR C 510 PHE 0.013 0.001 PHE B 318 TRP 0.011 0.001 TRP A 110 HIS 0.003 0.001 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (11238) covalent geometry : angle 0.55779 / 0.28 (15273) hydrogen bonds : bond 0.05319 / 3.56 ( 466) hydrogen bonds : angle 3.99842 / 2.78 ( 1350) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.421 Fit side-chains REVERT: B 261 MET cc_start: 0.7641 (mmp) cc_final: 0.6932 (mmp) REVERT: B 280 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8600 (tt) REVERT: B 293 ILE cc_start: 0.9054 (mm) cc_final: 0.8778 (mm) REVERT: B 424 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7322 (t80) REVERT: B 533 MET cc_start: 0.8730 (mtt) cc_final: 0.8363 (mtt) REVERT: C 17 GLU cc_start: 0.8459 (pm20) cc_final: 0.7497 (tm-30) REVERT: C 117 ARG cc_start: 0.8207 (mpt180) cc_final: 0.7737 (mmm-85) REVERT: C 119 ASP cc_start: 0.9246 (t0) cc_final: 0.8870 (t0) REVERT: C 146 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: C 272 MET cc_start: 0.8651 (mmp) cc_final: 0.8121 (mmp) REVERT: D 5 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7149 (mmtp) REVERT: D 37 LYS cc_start: 0.8099 (tttm) cc_final: 0.7788 (tptt) outliers start: 27 outliers final: 23 residues processed: 123 average time/residue: 0.0990 time to fit residues: 17.7845 Evaluate side-chains 125 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 109 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 95 optimal weight: 0.0670 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106190 restraints weight = 17471.574| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.34 r_work: 0.3248 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11239 Z= 0.097 Angle : 0.514 8.405 15273 Z= 0.258 Chirality : 0.041 0.220 1740 Planarity : 0.004 0.041 1904 Dihedral : 9.123 114.725 1740 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.51 % Allowed : 16.65 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1342 helix: 2.15 (0.22), residues: 608 sheet: 0.77 (0.52), residues: 114 loop : -1.48 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.014 0.001 TYR B 66 PHE 0.012 0.001 PHE D 54 TRP 0.011 0.001 TRP A 110 HIS 0.003 0.000 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (11238) covalent geometry : angle 0.51368 / 0.26 (15273) hydrogen bonds : bond 0.03708 / 2.48 ( 466) hydrogen bonds : angle 3.87706 / 2.70 ( 1350) Misc. bond : bond 0.00013 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.336 Fit side-chains REVERT: A 44 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7779 (ptmt) REVERT: B 261 MET cc_start: 0.7503 (mmp) cc_final: 0.6727 (mmp) REVERT: B 280 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8547 (tt) REVERT: B 293 ILE cc_start: 0.8975 (mm) cc_final: 0.8717 (mm) REVERT: B 424 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7063 (t80) REVERT: B 533 MET cc_start: 0.8651 (mtt) cc_final: 0.8304 (mtt) REVERT: C 17 GLU cc_start: 0.8448 (pm20) cc_final: 0.7507 (tm-30) REVERT: C 117 ARG cc_start: 0.8188 (mpt180) cc_final: 0.7727 (mmm-85) REVERT: C 119 ASP cc_start: 0.9231 (t0) cc_final: 0.8892 (t0) REVERT: C 146 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8406 (mt-10) REVERT: C 272 MET cc_start: 0.8612 (mmp) cc_final: 0.8103 (mmp) REVERT: D 5 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7185 (mmtp) outliers start: 18 outliers final: 14 residues processed: 120 average time/residue: 0.0967 time to fit residues: 16.6878 Evaluate side-chains 115 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 16 optimal weight: 0.0010 chunk 123 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100812 restraints weight = 18127.623| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.64 r_work: 0.3253 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11239 Z= 0.174 Angle : 0.606 9.611 15273 Z= 0.308 Chirality : 0.044 0.217 1740 Planarity : 0.004 0.042 1904 Dihedral : 9.345 115.025 1740 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.84 % Allowed : 17.07 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.23), residues: 1342 helix: 1.99 (0.22), residues: 614 sheet: 0.75 (0.47), residues: 134 loop : -1.58 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.019 0.001 TYR C 510 PHE 0.015 0.001 PHE B 318 TRP 0.011 0.001 TRP A 110 HIS 0.004 0.001 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (11238) covalent geometry : angle 0.60563 / 0.31 (15273) hydrogen bonds : bond 0.06033 / 4.05 ( 466) hydrogen bonds : angle 4.09156 / 2.84 ( 1350) Misc. bond : bond 0.00026 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.16 seconds wall clock time: 38 minutes 14.09 seconds (2294.09 seconds total)