Starting phenix.real_space_refine on Tue Jun 10 01:38:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c80_16467/06_2025/8c80_16467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c80_16467/06_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_16467/06_2025/8c80_16467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c80_16467/06_2025/8c80_16467.map" model { file = "/net/cci-nas-00/data/ceres_data/8c80_16467/06_2025/8c80_16467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c80_16467/06_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-5710/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: 7.90, per 1000 atoms: 0.72 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: 3.05 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: 1.05 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: 3.02 Time building geometry restraints manager: 3.20 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: 6.720 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: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.750 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- 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 : 1.174 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: 0.2463 time to fit residues: 81.1684 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 : 1.169 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106846 restraints weight = 17597.146| |-----------------------------------------------------------------------------| r_work (start): 0.3488 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 0.64553 (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 : 1.193 Fit side-chains REVERT: A 143 ASP cc_start: 0.8646 (t0) cc_final: 0.8432 (t0) REVERT: A 207 ARG cc_start: 0.8838 (mtp85) cc_final: 0.8510 (mtt-85) REVERT: B 91 GLN cc_start: 0.8158 (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: 0.7440 (tttm) cc_final: 0.7038 (tppt) outliers start: 21 outliers final: 11 residues processed: 144 average time/residue: 0.2499 time to fit residues: 50.3580 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 : 1.242 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.129952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107031 restraints weight = 17856.847| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.60 r_work: 0.3348 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11239 Z= 0.123 Angle : 0.579 8.272 15273 Z= 0.285 Chirality : 0.043 0.313 1740 Planarity : 0.004 0.042 1904 Dihedral : 10.667 113.322 1920 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.34 % Allowed : 12.80 % Favored : 84.85 % 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: 0.27 (0.23), residues: 1342 helix: 1.68 (0.22), residues: 611 sheet: 0.85 (0.49), residues: 118 loop : -1.60 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 188 HIS 0.008 0.001 HIS C 90 PHE 0.019 0.001 PHE D 62 TYR 0.016 0.001 TYR B 66 ARG 0.003 0.000 ARG C 9 Details of bonding type rmsd hydrogen bonds : bond 0.04964 ( 466) hydrogen bonds : angle 4.14701 ( 1350) covalent geometry : bond 0.00276 (11238) covalent geometry : angle 0.57927 (15273) Misc. bond : bond 0.00034 ( 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 147 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.198 Fit side-chains REVERT: A 143 ASP cc_start: 0.8523 (t0) cc_final: 0.8323 (t0) REVERT: A 207 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8417 (mtt-85) REVERT: B 92 GLU cc_start: 0.8515 (mp0) cc_final: 0.8170 (mt-10) REVERT: C 292 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7380 (mtp85) REVERT: C 405 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: C 424 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: D 7 SER cc_start: 0.8770 (t) cc_final: 0.8480 (p) REVERT: D 37 LYS cc_start: 0.7525 (tttm) cc_final: 0.7035 (tppt) outliers start: 28 outliers final: 16 residues processed: 139 average time/residue: 0.2285 time to fit residues: 45.8468 Evaluate side-chains 119 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 199 THR 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: 2.9990 chunk 111 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.0050 chunk 108 optimal weight: 2.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN C 143 ASN D 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.126699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103863 restraints weight = 17790.028| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.58 r_work: 0.3304 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4587 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= 0.137 Angle : 0.569 9.391 15273 Z= 0.287 Chirality : 0.043 0.230 1740 Planarity : 0.004 0.045 1904 Dihedral : 9.795 125.552 1920 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.85 % Allowed : 13.64 % Favored : 83.51 % 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: 0.39 (0.23), residues: 1342 helix: 1.87 (0.22), residues: 608 sheet: 0.82 (0.48), residues: 128 loop : -1.64 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 188 HIS 0.003 0.001 HIS C 514 PHE 0.014 0.001 PHE C 329 TYR 0.017 0.001 TYR C 510 ARG 0.003 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.05402 ( 466) hydrogen bonds : angle 4.08920 ( 1350) covalent geometry : bond 0.00321 (11238) covalent geometry : angle 0.56946 (15273) Misc. bond : bond 0.00040 ( 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 : 1.289 Fit side-chains REVERT: B 92 GLU cc_start: 0.8548 (mp0) cc_final: 0.8303 (mt-10) REVERT: B 261 MET cc_start: 0.7541 (mmp) cc_final: 0.6763 (mmp) REVERT: C 292 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7400 (mtp85) REVERT: C 405 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: D 5 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7018 (mmtp) REVERT: D 7 SER cc_start: 0.8801 (t) cc_final: 0.8494 (p) REVERT: D 37 LYS cc_start: 0.7741 (tttm) cc_final: 0.7398 (tppt) outliers start: 34 outliers final: 21 residues processed: 140 average time/residue: 0.2465 time to fit residues: 48.9213 Evaluate side-chains 125 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN C 143 ASN D 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097733 restraints weight = 18004.852| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.65 r_work: 0.3208 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 11239 Z= 0.230 Angle : 0.665 10.716 15273 Z= 0.344 Chirality : 0.046 0.212 1740 Planarity : 0.005 0.043 1904 Dihedral : 9.978 122.691 1920 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.43 % Allowed : 13.81 % 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: 0.12 (0.23), residues: 1342 helix: 1.65 (0.22), residues: 602 sheet: 0.92 (0.48), residues: 117 loop : -1.79 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 188 HIS 0.006 0.001 HIS C 203 PHE 0.021 0.002 PHE B 318 TYR 0.020 0.002 TYR C 510 ARG 0.005 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.07463 ( 466) hydrogen bonds : angle 4.38644 ( 1350) covalent geometry : bond 0.00568 (11238) covalent geometry : angle 0.66519 (15273) Misc. bond : bond 0.00039 ( 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 143 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 102 time to evaluate : 1.250 Fit side-chains REVERT: A 143 ASP cc_start: 0.8709 (t0) cc_final: 0.8410 (t0) REVERT: B 92 GLU cc_start: 0.8623 (mp0) cc_final: 0.8416 (mt-10) REVERT: B 261 MET cc_start: 0.7626 (mmp) cc_final: 0.7011 (mmp) REVERT: B 280 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8666 (tt) REVERT: B 533 MET cc_start: 0.8743 (mtt) cc_final: 0.8292 (mtt) REVERT: C 117 ARG cc_start: 0.8267 (mpt180) cc_final: 0.7676 (mmm-85) REVERT: C 239 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8236 (ttpp) REVERT: C 292 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7469 (mtp85) REVERT: C 405 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8413 (tp40) REVERT: D 37 LYS cc_start: 0.8028 (tttm) cc_final: 0.7649 (tppt) outliers start: 41 outliers final: 28 residues processed: 133 average time/residue: 0.2265 time to fit residues: 44.1908 Evaluate side-chains 128 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 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 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 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 395 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.0030 chunk 32 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 71 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 220 GLN 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 = 0.3752 r_free = 0.3752 target = 0.127560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104569 restraints weight = 17803.240| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.67 r_work: 0.3317 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11239 Z= 0.102 Angle : 0.521 9.261 15273 Z= 0.263 Chirality : 0.041 0.239 1740 Planarity : 0.004 0.040 1904 Dihedral : 9.527 122.445 1920 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.92 % Allowed : 15.31 % 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: 0.45 (0.23), residues: 1342 helix: 1.96 (0.22), residues: 604 sheet: 0.75 (0.51), residues: 116 loop : -1.58 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 110 HIS 0.006 0.001 HIS D 60 PHE 0.015 0.001 PHE C 329 TYR 0.015 0.001 TYR B 66 ARG 0.002 0.000 ARG C 9 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 466) hydrogen bonds : angle 3.99468 ( 1350) covalent geometry : bond 0.00215 (11238) covalent geometry : angle 0.52130 (15273) Misc. bond : bond 0.00013 ( 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 137 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8674 (t0) cc_final: 0.8348 (t0) REVERT: A 207 ARG cc_start: 0.8915 (mtp180) cc_final: 0.8705 (mtt-85) REVERT: B 261 MET cc_start: 0.7207 (mmp) cc_final: 0.6368 (mmp) REVERT: B 280 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8656 (tt) REVERT: B 533 MET cc_start: 0.8647 (mtt) cc_final: 0.8293 (mtt) REVERT: C 17 GLU cc_start: 0.8532 (pm20) cc_final: 0.7606 (tm-30) REVERT: C 117 ARG cc_start: 0.8175 (mpt180) cc_final: 0.7640 (mmm-85) REVERT: C 119 ASP cc_start: 0.9123 (t0) cc_final: 0.8578 (t0) REVERT: D 5 LYS cc_start: 0.7579 (mmmt) cc_final: 0.6998 (mmtp) REVERT: D 37 LYS cc_start: 0.7981 (tttm) cc_final: 0.7577 (tppt) outliers start: 23 outliers final: 13 residues processed: 133 average time/residue: 0.2426 time to fit residues: 45.7429 Evaluate side-chains 122 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 56 SER 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: 1.9990 chunk 128 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 258 HIS C 405 GLN D 60 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096342 restraints weight = 17949.485| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.39 r_work: 0.3112 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11239 Z= 0.255 Angle : 0.670 10.108 15273 Z= 0.346 Chirality : 0.047 0.223 1740 Planarity : 0.005 0.043 1904 Dihedral : 9.841 121.734 1920 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.10 % Allowed : 14.48 % 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: 0.11 (0.23), residues: 1342 helix: 1.66 (0.22), residues: 607 sheet: 0.70 (0.48), residues: 119 loop : -1.79 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 110 HIS 0.006 0.001 HIS A 206 PHE 0.022 0.002 PHE B 318 TYR 0.020 0.002 TYR C 510 ARG 0.005 0.001 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.07519 ( 466) hydrogen bonds : angle 4.34981 ( 1350) covalent geometry : bond 0.00640 (11238) covalent geometry : angle 0.67007 (15273) Misc. bond : bond 0.00050 ( 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: 37 poor density : 104 time to evaluate : 1.188 Fit side-chains REVERT: A 143 ASP cc_start: 0.8863 (t0) cc_final: 0.8618 (t0) REVERT: B 261 MET cc_start: 0.7773 (mmp) cc_final: 0.7172 (mmp) REVERT: B 280 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8658 (tt) REVERT: B 533 MET cc_start: 0.8771 (mtt) cc_final: 0.8393 (mtt) REVERT: C 117 ARG cc_start: 0.8299 (mpt180) cc_final: 0.7672 (mmm160) REVERT: C 239 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8304 (ttpp) REVERT: D 5 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7122 (mmtp) REVERT: D 37 LYS cc_start: 0.8134 (tttm) cc_final: 0.7723 (tppt) outliers start: 37 outliers final: 29 residues processed: 130 average time/residue: 0.2356 time to fit residues: 44.0455 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 : 1.191 ------------------------------------------------------------------------------- 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 32 VAL 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 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 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 38 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 127 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102722 restraints weight = 17336.673| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.26 r_work: 0.3224 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11239 Z= 0.110 Angle : 0.536 8.873 15273 Z= 0.272 Chirality : 0.042 0.208 1740 Planarity : 0.004 0.040 1904 Dihedral : 9.460 120.107 1920 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.18 % Allowed : 15.73 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.23), residues: 1342 helix: 1.91 (0.22), residues: 608 sheet: 0.53 (0.51), residues: 116 loop : -1.67 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 110 HIS 0.003 0.001 HIS A 206 PHE 0.013 0.001 PHE C 329 TYR 0.016 0.001 TYR B 66 ARG 0.002 0.000 ARG C 9 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 466) hydrogen bonds : angle 4.02591 ( 1350) covalent geometry : bond 0.00244 (11238) covalent geometry : angle 0.53621 (15273) Misc. bond : bond 0.00019 ( 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 130 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: B 261 MET cc_start: 0.7471 (mmp) cc_final: 0.6745 (mmp) REVERT: B 280 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8693 (tt) REVERT: B 533 MET cc_start: 0.8718 (mtt) cc_final: 0.8380 (mtt) REVERT: C 17 GLU cc_start: 0.8450 (pm20) cc_final: 0.7539 (tm-30) REVERT: C 117 ARG cc_start: 0.8239 (mpt180) cc_final: 0.7733 (mmm160) REVERT: C 119 ASP cc_start: 0.9256 (t0) cc_final: 0.8832 (t0) REVERT: C 239 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8121 (ttpp) REVERT: D 5 LYS cc_start: 0.7718 (mmmt) cc_final: 0.7147 (mmtp) REVERT: D 37 LYS cc_start: 0.8149 (tttm) cc_final: 0.7843 (tptt) outliers start: 26 outliers final: 23 residues processed: 122 average time/residue: 0.3062 time to fit residues: 53.0699 Evaluate side-chains 125 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 32 VAL 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 C residue 74 LEU 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 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 34 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100547 restraints weight = 17743.830| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.30 r_work: 0.3174 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11239 Z= 0.131 Angle : 0.551 9.206 15273 Z= 0.280 Chirality : 0.042 0.206 1740 Planarity : 0.004 0.041 1904 Dihedral : 9.407 118.690 1920 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.84 % Allowed : 16.49 % Favored : 81.67 % 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: 0.38 (0.23), residues: 1342 helix: 1.94 (0.22), residues: 609 sheet: 0.47 (0.51), residues: 118 loop : -1.64 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.003 0.001 HIS A 206 PHE 0.012 0.001 PHE C 329 TYR 0.016 0.001 TYR C 510 ARG 0.002 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.05102 ( 466) hydrogen bonds : angle 4.02096 ( 1350) covalent geometry : bond 0.00310 (11238) covalent geometry : angle 0.55091 (15273) Misc. bond : bond 0.00026 ( 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 124 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 125 VAL cc_start: 0.8759 (p) cc_final: 0.8536 (p) REVERT: B 261 MET cc_start: 0.7476 (mmp) cc_final: 0.6747 (mmp) REVERT: B 280 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8648 (tt) REVERT: B 424 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 533 MET cc_start: 0.8728 (mtt) cc_final: 0.8357 (mtt) REVERT: C 17 GLU cc_start: 0.8436 (pm20) cc_final: 0.7536 (tm-30) REVERT: C 117 ARG cc_start: 0.8292 (mpt180) cc_final: 0.7776 (mmm160) REVERT: C 119 ASP cc_start: 0.9278 (t0) cc_final: 0.8857 (t0) REVERT: D 5 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7152 (mmtp) REVERT: D 37 LYS cc_start: 0.8122 (tttm) cc_final: 0.7832 (tptt) outliers start: 22 outliers final: 20 residues processed: 118 average time/residue: 0.2815 time to fit residues: 47.2284 Evaluate side-chains 122 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 32 VAL 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 C residue 74 LEU 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 412 THR Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain D residue 34 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 0.0970 chunk 66 optimal weight: 0.0270 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105628 restraints weight = 17811.215| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.63 r_work: 0.3329 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11239 Z= 0.101 Angle : 0.517 8.536 15273 Z= 0.261 Chirality : 0.041 0.207 1740 Planarity : 0.004 0.040 1904 Dihedral : 9.172 116.119 1920 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.84 % Allowed : 16.32 % 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: 0.57 (0.23), residues: 1342 helix: 2.08 (0.22), residues: 608 sheet: 0.70 (0.52), residues: 116 loop : -1.54 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.002 0.001 HIS C 514 PHE 0.011 0.001 PHE C 329 TYR 0.014 0.001 TYR B 66 ARG 0.002 0.000 ARG C 9 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 466) hydrogen bonds : angle 3.89727 ( 1350) covalent geometry : bond 0.00227 (11238) covalent geometry : angle 0.51693 (15273) Misc. bond : bond 0.00016 ( 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 126 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 207 ARG cc_start: 0.8925 (mtp85) cc_final: 0.8568 (mtt-85) REVERT: B 261 MET cc_start: 0.7201 (mmp) cc_final: 0.6416 (mmp) REVERT: B 280 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8652 (tt) REVERT: B 424 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7002 (t80) REVERT: B 533 MET cc_start: 0.8609 (mtt) cc_final: 0.8233 (mtt) REVERT: C 17 GLU cc_start: 0.8435 (pm20) cc_final: 0.7532 (tm-30) REVERT: C 117 ARG cc_start: 0.8211 (mpt180) cc_final: 0.7663 (mmm160) REVERT: C 119 ASP cc_start: 0.9207 (t0) cc_final: 0.8812 (t0) REVERT: C 292 ARG cc_start: 0.7945 (mtp85) cc_final: 0.7558 (mtp85) REVERT: C 473 MET cc_start: 0.8684 (mmm) cc_final: 0.8297 (mmt) REVERT: D 5 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7022 (mmtp) outliers start: 22 outliers final: 19 residues processed: 120 average time/residue: 0.2456 time to fit residues: 42.6342 Evaluate side-chains 122 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 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 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 34 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 69 optimal weight: 2.9990 chunk 128 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105360 restraints weight = 17758.742| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.63 r_work: 0.3325 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 11239 Z= 0.157 Angle : 0.814 59.199 15273 Z= 0.475 Chirality : 0.050 1.181 1740 Planarity : 0.004 0.065 1904 Dihedral : 9.182 116.113 1920 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 1.92 % Allowed : 16.57 % Favored : 81.51 % 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: 0.57 (0.23), residues: 1342 helix: 2.09 (0.22), residues: 608 sheet: 0.71 (0.52), residues: 116 loop : -1.55 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.007 0.001 HIS A 46 PHE 0.011 0.001 PHE C 329 TYR 0.014 0.001 TYR B 66 ARG 0.004 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 466) hydrogen bonds : angle 3.89664 ( 1350) covalent geometry : bond 0.00315 (11238) covalent geometry : angle 0.81439 (15273) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5283.17 seconds wall clock time: 94 minutes 6.82 seconds (5646.82 seconds total)