Starting phenix.real_space_refine on Wed May 14 00:49:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c80_16467/05_2025/8c80_16467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c80_16467/05_2025/8c80_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c80_16467/05_2025/8c80_16467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c80_16467/05_2025/8c80_16467.map" model { file = "/net/cci-nas-00/data/ceres_data/8c80_16467/05_2025/8c80_16467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c80_16467/05_2025/8c80_16467.cif" } resolution = 3.4 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= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.49, per 1000 atoms: 0.77 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: 3.01 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.29 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: 2.96 Time building geometry restraints manager: 3.41 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: 6746 27.51 - 55.01: 231 55.01 - 82.52: 35 82.52 - 110.03: 16 110.03 - 137.53: 12 Dihedral angle restraints: 7040 sinusoidal: 3090 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 7037 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.880 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 15.812 137.534 4498 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.41 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 (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: -1.48 (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 TRP 0.009 0.001 TRP C 102 HIS 0.010 0.001 HIS A 206 PHE 0.013 0.001 PHE C 109 TYR 0.028 0.002 TYR B 186 ARG 0.004 0.001 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.28392 ( 466) hydrogen bonds : angle 7.74949 ( 1350) covalent geometry : bond 0.00562 (11238) covalent geometry : angle 0.84761 (15273) Misc. bond : bond 0.03814 ( 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 : 1.167 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: 0.7334 (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: 0.2600 time to fit residues: 85.4100 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 : 1.328 ------------------------------------------------------------------------------- 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 112 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 180 HIS B 50 HIS C 90 HIS C 142 HIS C 145 ASN C 170 GLN C 229 ASN C 291 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.130906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106858 restraints weight = 17597.152| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.71 r_work: 0.3351 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11239 Z= 0.153 Angle : 0.646 11.443 15273 Z= 0.323 Chirality : 0.044 0.242 1740 Planarity : 0.005 0.043 1904 Dihedral : 12.840 124.847 1923 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.76 % Allowed : 12.05 % Favored : 86.19 % 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: -0.17 (0.22), residues: 1342 helix: 1.20 (0.21), residues: 612 sheet: 0.84 (0.49), residues: 116 loop : -1.74 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.006 0.001 HIS C 96 PHE 0.025 0.001 PHE C 106 TYR 0.022 0.001 TYR B 66 ARG 0.004 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.06228 ( 466) hydrogen bonds : angle 4.62629 ( 1350) covalent geometry : bond 0.00338 (11238) covalent geometry : angle 0.64554 (15273) Misc. bond : bond 0.00017 ( 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 152 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.202 Fit side-chains REVERT: A 143 ASP cc_start: 0.8646 (t0) cc_final: 0.8431 (t0) REVERT: A 207 ARG cc_start: 0.8838 (mtp85) cc_final: 0.8510 (mtt-85) REVERT: B 91 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7673 (mp10) REVERT: C 292 ARG cc_start: 0.7711 (mtp85) cc_final: 0.7240 (mtp85) REVERT: D 7 SER cc_start: 0.8765 (t) cc_final: 0.8509 (p) REVERT: D 37 LYS cc_start: 0.7442 (tttm) cc_final: 0.7041 (tppt) outliers start: 21 outliers final: 11 residues processed: 144 average time/residue: 0.2619 time to fit residues: 52.5607 Evaluate side-chains 112 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 75 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 129 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN C 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106315 restraints weight = 17904.151| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.69 r_work: 0.3335 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11239 Z= 0.129 Angle : 0.586 8.611 15273 Z= 0.289 Chirality : 0.043 0.323 1740 Planarity : 0.004 0.042 1904 Dihedral : 10.603 113.044 1920 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.34 % Allowed : 12.72 % Favored : 84.94 % 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: 0.25 (0.23), residues: 1342 helix: 1.65 (0.22), residues: 613 sheet: 0.84 (0.49), residues: 118 loop : -1.61 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 188 HIS 0.007 0.001 HIS C 90 PHE 0.020 0.001 PHE D 62 TYR 0.017 0.001 TYR B 66 ARG 0.004 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 466) hydrogen bonds : angle 4.15453 ( 1350) covalent geometry : bond 0.00289 (11238) covalent geometry : angle 0.58606 (15273) Misc. bond : bond 0.00038 ( 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 148 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: C 292 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7400 (mtp85) REVERT: C 405 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: C 424 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8246 (tm-30) REVERT: D 7 SER cc_start: 0.8785 (t) cc_final: 0.8490 (p) REVERT: D 37 LYS cc_start: 0.7537 (tttm) cc_final: 0.7043 (tppt) outliers start: 28 outliers final: 16 residues processed: 140 average time/residue: 0.2323 time to fit residues: 46.8151 Evaluate side-chains 121 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 154 GLU 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 552 CYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 86 GLN 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 357 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 C residue 466 MET 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 16 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 120 optimal weight: 0.0370 chunk 88 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 220 GLN C 143 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 = 0.3750 r_free = 0.3750 target = 0.127222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104470 restraints weight = 17746.811| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.57 r_work: 0.3313 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4503 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= 0.129 Angle : 0.556 9.253 15273 Z= 0.279 Chirality : 0.043 0.231 1740 Planarity : 0.004 0.044 1904 Dihedral : 9.746 123.634 1920 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.85 % Allowed : 13.31 % Favored : 83.85 % 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: 0.41 (0.23), residues: 1342 helix: 1.89 (0.22), residues: 608 sheet: 0.78 (0.50), residues: 118 loop : -1.60 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 188 HIS 0.003 0.001 HIS C 514 PHE 0.014 0.001 PHE C 329 TYR 0.016 0.001 TYR B 66 ARG 0.003 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 466) hydrogen bonds : angle 4.05793 ( 1350) covalent geometry : bond 0.00301 (11238) covalent geometry : angle 0.55584 (15273) Misc. bond : bond 0.00033 ( 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 150 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.233 Fit side-chains REVERT: B 92 GLU cc_start: 0.8544 (mp0) cc_final: 0.8292 (mt-10) REVERT: B 261 MET cc_start: 0.7521 (mmp) cc_final: 0.6687 (mmp) REVERT: C 272 MET cc_start: 0.8566 (mmp) cc_final: 0.7800 (mmt) REVERT: C 292 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7371 (mtp85) REVERT: C 405 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: D 5 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7042 (mmtp) REVERT: D 7 SER cc_start: 0.8756 (t) cc_final: 0.8432 (p) REVERT: D 37 LYS cc_start: 0.7679 (tttm) cc_final: 0.7333 (tppt) outliers start: 34 outliers final: 20 residues processed: 140 average time/residue: 0.2449 time to fit residues: 49.0010 Evaluate side-chains 126 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 A residue 215 ILE Chi-restraints excluded: chain B residue 69 ILE 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 C residue 84 THR Chi-restraints excluded: chain C residue 91 LEU 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 260 SER 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 65 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3697 r_free = 0.3697 target = 0.123518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100082 restraints weight = 17842.963| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.66 r_work: 0.3246 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11239 Z= 0.173 Angle : 0.606 9.514 15273 Z= 0.311 Chirality : 0.044 0.205 1740 Planarity : 0.004 0.043 1904 Dihedral : 9.794 123.385 1920 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.35 % Allowed : 13.47 % Favored : 83.18 % 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: 0.30 (0.23), residues: 1342 helix: 1.80 (0.22), residues: 605 sheet: 0.82 (0.46), residues: 126 loop : -1.70 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 188 HIS 0.004 0.001 HIS C 203 PHE 0.018 0.001 PHE B 318 TYR 0.017 0.001 TYR C 510 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.06383 ( 466) hydrogen bonds : angle 4.19668 ( 1350) covalent geometry : bond 0.00417 (11238) covalent geometry : angle 0.60604 (15273) Misc. bond : bond 0.00044 ( 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: 40 poor density : 109 time to evaluate : 1.342 Fit side-chains REVERT: A 143 ASP cc_start: 0.8648 (t0) cc_final: 0.8314 (t0) REVERT: B 92 GLU cc_start: 0.8578 (mp0) cc_final: 0.8368 (mt-10) REVERT: B 261 MET cc_start: 0.7540 (mmp) cc_final: 0.6882 (mmp) REVERT: B 280 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8623 (tt) REVERT: B 533 MET cc_start: 0.8671 (mtt) cc_final: 0.8247 (mtt) REVERT: C 17 GLU cc_start: 0.8565 (pm20) cc_final: 0.7872 (tm-30) REVERT: C 119 ASP cc_start: 0.8997 (t0) cc_final: 0.8523 (t0) REVERT: C 146 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8329 (mt-10) REVERT: C 292 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7377 (mtp85) REVERT: C 405 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8372 (tp40) REVERT: D 37 LYS cc_start: 0.7899 (tttm) cc_final: 0.7535 (tppt) outliers start: 40 outliers final: 28 residues processed: 138 average time/residue: 0.2264 time to fit residues: 45.7864 Evaluate side-chains 135 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 153 ASP 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 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 91 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 260 SER 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 C residue 560 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 37 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 144 ASN C 143 ASN D 29 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 = 0.3718 r_free = 0.3718 target = 0.125126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101900 restraints weight = 17924.067| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.68 r_work: 0.3276 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11239 Z= 0.131 Angle : 0.549 9.275 15273 Z= 0.279 Chirality : 0.042 0.229 1740 Planarity : 0.004 0.042 1904 Dihedral : 9.592 122.297 1920 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.68 % Allowed : 14.48 % Favored : 82.85 % 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: 0.37 (0.23), residues: 1342 helix: 1.90 (0.22), residues: 606 sheet: 0.62 (0.51), residues: 118 loop : -1.64 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 110 HIS 0.005 0.001 HIS D 60 PHE 0.013 0.001 PHE C 329 TYR 0.017 0.001 TYR B 66 ARG 0.005 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.05237 ( 466) hydrogen bonds : angle 4.04913 ( 1350) covalent geometry : bond 0.00309 (11238) covalent geometry : angle 0.54900 (15273) Misc. bond : bond 0.00030 ( 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 141 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 1.294 Fit side-chains REVERT: A 143 ASP cc_start: 0.8754 (t0) cc_final: 0.8438 (t0) REVERT: B 261 MET cc_start: 0.7370 (mmp) cc_final: 0.6640 (mmp) REVERT: B 280 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (tt) REVERT: B 533 MET cc_start: 0.8648 (mtt) cc_final: 0.8277 (mtt) REVERT: C 119 ASP cc_start: 0.9065 (t0) cc_final: 0.8473 (t0) REVERT: C 146 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8401 (mt-10) REVERT: C 405 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8351 (tp40) REVERT: D 37 LYS cc_start: 0.7957 (tttm) cc_final: 0.7579 (tppt) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 0.2431 time to fit residues: 46.0355 Evaluate side-chains 130 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 185 PHE Chi-restraints excluded: chain B residue 205 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 74 LEU 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 357 VAL 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 53 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 93 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 HIS D 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102729 restraints weight = 17767.417| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.29 r_work: 0.3222 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11239 Z= 0.126 Angle : 0.543 8.973 15273 Z= 0.276 Chirality : 0.042 0.225 1740 Planarity : 0.004 0.042 1904 Dihedral : 9.472 120.580 1920 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.85 % Allowed : 14.39 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.23), residues: 1342 helix: 1.94 (0.22), residues: 609 sheet: 0.71 (0.51), residues: 116 loop : -1.61 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.005 0.001 HIS D 60 PHE 0.013 0.001 PHE C 329 TYR 0.016 0.001 TYR B 66 ARG 0.008 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 466) hydrogen bonds : angle 4.00279 ( 1350) covalent geometry : bond 0.00298 (11238) covalent geometry : angle 0.54313 (15273) Misc. bond : bond 0.00027 ( 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 141 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 1.180 Fit side-chains REVERT: A 143 ASP cc_start: 0.8828 (t0) cc_final: 0.8549 (t0) REVERT: B 261 MET cc_start: 0.7530 (mmp) cc_final: 0.6866 (mmp) REVERT: B 280 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8627 (tt) REVERT: B 533 MET cc_start: 0.8738 (mtt) cc_final: 0.8380 (mtt) REVERT: C 17 GLU cc_start: 0.8527 (pm20) cc_final: 0.7575 (tm-30) REVERT: C 117 ARG cc_start: 0.8182 (mpt180) cc_final: 0.7758 (mmm-85) REVERT: C 119 ASP cc_start: 0.9196 (t0) cc_final: 0.8672 (t0) REVERT: C 146 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8420 (mt-10) REVERT: D 37 LYS cc_start: 0.8207 (tttm) cc_final: 0.7806 (tppt) outliers start: 34 outliers final: 28 residues processed: 134 average time/residue: 0.2136 time to fit residues: 41.7048 Evaluate side-chains 132 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 357 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 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 chunk 127 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102668 restraints weight = 17459.089| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.27 r_work: 0.3206 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11239 Z= 0.130 Angle : 0.544 8.876 15273 Z= 0.276 Chirality : 0.042 0.218 1740 Planarity : 0.004 0.041 1904 Dihedral : 9.383 119.028 1920 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.68 % Allowed : 14.90 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1342 helix: 1.98 (0.22), residues: 609 sheet: 0.60 (0.51), residues: 118 loop : -1.61 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.003 0.001 HIS C 203 PHE 0.012 0.001 PHE C 329 TYR 0.016 0.001 TYR B 66 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 466) hydrogen bonds : angle 4.00299 ( 1350) covalent geometry : bond 0.00307 (11238) covalent geometry : angle 0.54384 (15273) Misc. bond : bond 0.00028 ( 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 136 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 1.239 Fit side-chains REVERT: B 261 MET cc_start: 0.7509 (mmp) cc_final: 0.6855 (mmp) REVERT: B 280 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8606 (tt) REVERT: B 424 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7169 (t80) REVERT: B 533 MET cc_start: 0.8717 (mtt) cc_final: 0.8360 (mtt) REVERT: C 17 GLU cc_start: 0.8560 (pm20) cc_final: 0.7604 (tm-30) REVERT: C 117 ARG cc_start: 0.8168 (mpt180) cc_final: 0.7794 (mmm-85) REVERT: C 119 ASP cc_start: 0.9221 (t0) cc_final: 0.8740 (t0) REVERT: C 146 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8354 (mt-10) REVERT: D 37 LYS cc_start: 0.8093 (tttm) cc_final: 0.7679 (tppt) outliers start: 32 outliers final: 28 residues processed: 130 average time/residue: 0.2254 time to fit residues: 42.5513 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 : 1.195 ------------------------------------------------------------------------------- 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 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 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 162 SER Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 357 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 53 SER 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 2 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 85 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 0.0670 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105171 restraints weight = 17626.851| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.26 r_work: 0.3275 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11239 Z= 0.101 Angle : 0.514 8.227 15273 Z= 0.260 Chirality : 0.041 0.221 1740 Planarity : 0.004 0.041 1904 Dihedral : 9.160 116.240 1920 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.84 % Allowed : 15.98 % Favored : 82.18 % 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: 0.60 (0.23), residues: 1342 helix: 2.11 (0.22), residues: 607 sheet: 0.76 (0.52), residues: 116 loop : -1.53 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.002 0.001 HIS C 514 PHE 0.012 0.001 PHE C 329 TYR 0.014 0.001 TYR B 66 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 466) hydrogen bonds : angle 3.88684 ( 1350) covalent geometry : bond 0.00228 (11238) covalent geometry : angle 0.51395 (15273) Misc. bond : bond 0.00016 ( 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 137 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.157 Fit side-chains REVERT: A 44 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7703 (ptmt) REVERT: B 261 MET cc_start: 0.7476 (mmp) cc_final: 0.6759 (mmp) REVERT: B 280 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8614 (tt) REVERT: B 424 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7059 (t80) REVERT: B 533 MET cc_start: 0.8677 (mtt) cc_final: 0.8336 (mtt) REVERT: C 17 GLU cc_start: 0.8509 (pm20) cc_final: 0.7651 (tm-30) REVERT: C 117 ARG cc_start: 0.8169 (mpt180) cc_final: 0.7700 (mmm160) REVERT: C 119 ASP cc_start: 0.9213 (t0) cc_final: 0.8765 (t0) REVERT: C 146 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8416 (mt-10) REVERT: C 290 THR cc_start: 0.8740 (m) cc_final: 0.8509 (m) REVERT: D 37 LYS cc_start: 0.8112 (tttm) cc_final: 0.7808 (tptt) outliers start: 22 outliers final: 19 residues processed: 133 average time/residue: 0.2388 time to fit residues: 45.9166 Evaluate side-chains 123 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 78 HIS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 172 LYS 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 41 THR Chi-restraints excluded: chain D residue 53 SER 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 10 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.0000 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 0.0010 chunk 132 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS D 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.129196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106180 restraints weight = 17821.003| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.66 r_work: 0.3333 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11239 Z= 0.104 Angle : 0.525 8.527 15273 Z= 0.265 Chirality : 0.041 0.220 1740 Planarity : 0.004 0.041 1904 Dihedral : 9.030 113.793 1920 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.76 % Allowed : 16.40 % 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 (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: 0.72 (0.23), residues: 1342 helix: 2.18 (0.22), residues: 608 sheet: 0.86 (0.52), residues: 116 loop : -1.44 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.002 0.001 HIS C 514 PHE 0.012 0.001 PHE C 329 TYR 0.014 0.001 TYR B 66 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 466) hydrogen bonds : angle 3.85207 ( 1350) covalent geometry : bond 0.00233 (11238) covalent geometry : angle 0.52511 (15273) Misc. bond : bond 0.00014 ( 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 124 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.316 Fit side-chains REVERT: A 44 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7818 (ptmt) REVERT: B 261 MET cc_start: 0.7287 (mmp) cc_final: 0.6621 (mmp) REVERT: B 280 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8583 (tt) REVERT: B 424 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7042 (t80) REVERT: B 533 MET cc_start: 0.8605 (mtt) cc_final: 0.8242 (mtt) REVERT: C 17 GLU cc_start: 0.8505 (pm20) cc_final: 0.7674 (tm-30) REVERT: C 117 ARG cc_start: 0.8145 (mpt180) cc_final: 0.7745 (mmm-85) REVERT: C 119 ASP cc_start: 0.9153 (t0) cc_final: 0.8696 (t0) REVERT: C 146 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8316 (mt-10) REVERT: C 473 MET cc_start: 0.8659 (mmm) cc_final: 0.8185 (mmt) outliers start: 21 outliers final: 17 residues processed: 120 average time/residue: 0.2567 time to fit residues: 44.6205 Evaluate side-chains 119 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 172 LYS 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 53 SER 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 69 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.104491 restraints weight = 17274.616| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.48 r_work: 0.3318 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11239 Z= 0.123 Angle : 0.552 8.657 15273 Z= 0.281 Chirality : 0.042 0.218 1740 Planarity : 0.004 0.041 1904 Dihedral : 8.993 112.307 1920 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.51 % Allowed : 16.99 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.71 (0.23), residues: 1342 helix: 2.18 (0.22), residues: 607 sheet: 0.87 (0.52), residues: 116 loop : -1.45 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.014 0.001 HIS D 60 PHE 0.012 0.001 PHE C 329 TYR 0.016 0.001 TYR B 66 ARG 0.006 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 466) hydrogen bonds : angle 3.90321 ( 1350) covalent geometry : bond 0.00288 (11238) covalent geometry : angle 0.55208 (15273) Misc. bond : bond 0.00023 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4763.61 seconds wall clock time: 83 minutes 42.00 seconds (5022.00 seconds total)