Starting phenix.real_space_refine on Thu Mar 13 19:47:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdk_14652/03_2025/7zdk_14652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdk_14652/03_2025/7zdk_14652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zdk_14652/03_2025/7zdk_14652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdk_14652/03_2025/7zdk_14652.map" model { file = "/net/cci-nas-00/data/ceres_data/7zdk_14652/03_2025/7zdk_14652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdk_14652/03_2025/7zdk_14652.cif" } resolution = 3.01 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= 0.007 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 5804 2.51 5 N 1600 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9089 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "D" Number of atoms: 4592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4592 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.99, per 1000 atoms: 0.66 Number of scatterers: 9089 At special positions: 0 Unit cell: (117.18, 80.352, 114.669, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 6 15.00 Mg 2 11.99 O 1647 8.00 N 1600 7.00 C 5804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 68.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 14 through 50 Processing helix chain 'C' and resid 59 through 104 removed outlier: 3.556A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 132 removed outlier: 3.513A pdb=" N LEU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 137 through 157 removed outlier: 3.849A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 176 removed outlier: 3.612A pdb=" N THR C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 185 through 209 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 218 through 269 removed outlier: 3.586A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 269 " --> pdb=" O MET C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 290 removed outlier: 4.347A pdb=" N ALA C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 294 through 319 removed outlier: 4.335A pdb=" N GLY C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 300 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLN C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 387 removed outlier: 3.665A pdb=" N GLN C 385 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 408 through 415 Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.815A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 456 through 460 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.622A pdb=" N ASN C 465 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 466 " --> pdb=" O GLY C 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 466' Processing helix chain 'C' and resid 476 through 492 removed outlier: 3.675A pdb=" N LEU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.675A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 Processing helix chain 'C' and resid 564 through 572 Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.556A pdb=" N GLU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 15 " --> pdb=" O ARG D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 54 removed outlier: 3.584A pdb=" N PHE D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 110 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 133 through 139 removed outlier: 3.620A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 162 removed outlier: 3.670A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Proline residue: D 160 - end of helix Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.605A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 203 removed outlier: 3.643A pdb=" N LEU D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 274 removed outlier: 3.784A pdb=" N GLU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 310 removed outlier: 3.532A pdb=" N GLY D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 4.098A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.538A pdb=" N THR D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 330 removed outlier: 3.795A pdb=" N ALA D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.598A pdb=" N THR D 477 " --> pdb=" O GLY D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 501 Processing helix chain 'D' and resid 517 through 532 Processing helix chain 'D' and resid 566 through 573 removed outlier: 3.739A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 583 Processing sheet with id=AA1, first strand: chain 'C' and resid 362 through 363 Processing sheet with id=AA2, first strand: chain 'C' and resid 344 through 347 removed outlier: 6.709A pdb=" N VAL C 344 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS C 357 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE C 346 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.455A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 552 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP C 546 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.477A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.477A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 425 through 428 removed outlier: 6.889A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ASP D 510 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL D 428 " --> pdb=" O ASP D 510 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG D 378 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TRP D 554 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL D 380 " --> pdb=" O TRP D 554 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET D 556 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 553 " --> pdb=" O GLN D 564 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN D 564 " --> pdb=" O ILE D 553 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1677 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: 2.90 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2482 1.33 - 1.45: 1557 1.45 - 1.57: 5163 1.57 - 1.69: 10 1.69 - 1.81: 57 Bond restraints: 9269 Sorted by residual: bond pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 1.795 1.626 0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" N3B ANP C 602 " pdb=" PG ANP C 602 " ideal model delta sigma weight residual 1.795 1.628 0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" O3A ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sigma weight residual 1.700 1.596 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" N GLU C 500 " pdb=" CA GLU C 500 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.69e+01 ... (remaining 9264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 12316 2.27 - 4.55: 242 4.55 - 6.82: 38 6.82 - 9.09: 7 9.09 - 11.36: 1 Bond angle restraints: 12604 Sorted by residual: angle pdb=" N GLU C 515 " pdb=" CA GLU C 515 " pdb=" C GLU C 515 " ideal model delta sigma weight residual 111.36 105.54 5.82 1.09e+00 8.42e-01 2.86e+01 angle pdb=" C GLU C 500 " pdb=" CA GLU C 500 " pdb=" CB GLU C 500 " ideal model delta sigma weight residual 111.00 114.48 -3.48 8.70e-01 1.32e+00 1.60e+01 angle pdb=" N TYR C 11 " pdb=" CA TYR C 11 " pdb=" C TYR C 11 " ideal model delta sigma weight residual 112.89 108.04 4.85 1.24e+00 6.50e-01 1.53e+01 angle pdb=" N LYS C 12 " pdb=" CA LYS C 12 " pdb=" C LYS C 12 " ideal model delta sigma weight residual 111.28 107.08 4.20 1.09e+00 8.42e-01 1.48e+01 angle pdb=" N ARG D 11 " pdb=" CA ARG D 11 " pdb=" C ARG D 11 " ideal model delta sigma weight residual 111.82 107.40 4.42 1.16e+00 7.43e-01 1.45e+01 ... (remaining 12599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.57: 5037 19.57 - 39.13: 412 39.13 - 58.70: 71 58.70 - 78.27: 26 78.27 - 97.83: 18 Dihedral angle restraints: 5564 sinusoidal: 2233 harmonic: 3331 Sorted by residual: dihedral pdb=" CA LEU D 209 " pdb=" C LEU D 209 " pdb=" N ARG D 210 " pdb=" CA ARG D 210 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" O2' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 47.90 -49.93 97.83 1 3.00e+01 1.11e-03 1.21e+01 dihedral pdb=" C1' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 164.59 69.72 94.87 1 3.00e+01 1.11e-03 1.16e+01 ... (remaining 5561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1348 0.089 - 0.179: 103 0.179 - 0.268: 8 0.268 - 0.357: 0 0.357 - 0.446: 2 Chirality restraints: 1461 Sorted by residual: chirality pdb=" C3' ANP C 602 " pdb=" C2' ANP C 602 " pdb=" C4' ANP C 602 " pdb=" O3' ANP C 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.80 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" C3' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C4' ANP D 602 " pdb=" O3' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.80 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA VAL D 428 " pdb=" N VAL D 428 " pdb=" C VAL D 428 " pdb=" CB VAL D 428 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1458 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 428 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C VAL D 428 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL D 428 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY D 429 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 497 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C LEU C 497 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU C 497 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU C 498 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 511 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO D 512 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 512 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 512 " 0.022 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1431 2.75 - 3.29: 8840 3.29 - 3.83: 14871 3.83 - 4.36: 19151 4.36 - 4.90: 32283 Nonbonded interactions: 76576 Sorted by model distance: nonbonded pdb=" OG1 THR D 438 " pdb=" OD1 ASP D 441 " model vdw 2.219 3.040 nonbonded pdb="MG MG D 601 " pdb=" O1G ANP D 602 " model vdw 2.220 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1B ANP C 602 " model vdw 2.222 2.170 nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 2.223 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2G ANP C 602 " model vdw 2.224 2.170 ... (remaining 76571 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.650 Find NCS groups from input model: 0.140 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.007 0.169 9269 Z= 0.432 Angle : 0.783 11.363 12604 Z= 0.460 Chirality : 0.051 0.446 1461 Planarity : 0.004 0.040 1604 Dihedral : 16.142 97.831 3416 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.23), residues: 1157 helix: -1.19 (0.18), residues: 723 sheet: 0.39 (0.63), residues: 62 loop : -0.40 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 81 HIS 0.004 0.001 HIS C 14 PHE 0.014 0.002 PHE D 467 TYR 0.012 0.002 TYR D 88 ARG 0.008 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.693 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3776 time to fit residues: 55.1173 Evaluate side-chains 104 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN D 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.112793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.090432 restraints weight = 11067.447| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.52 r_work: 0.2818 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9269 Z= 0.220 Angle : 0.597 7.012 12604 Z= 0.305 Chirality : 0.041 0.152 1461 Planarity : 0.004 0.042 1604 Dihedral : 10.304 73.234 1329 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.06 % Allowed : 5.51 % Favored : 93.43 % 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: 0.47 (0.24), residues: 1157 helix: 0.75 (0.19), residues: 721 sheet: 0.30 (0.62), residues: 62 loop : -0.34 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 427 HIS 0.003 0.001 HIS D 51 PHE 0.014 0.001 PHE C 164 TYR 0.013 0.001 TYR D 88 ARG 0.005 0.000 ARG D 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.973 Fit side-chains REVERT: D 154 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8571 (mt) REVERT: D 207 ASP cc_start: 0.8233 (t0) cc_final: 0.7924 (t0) REVERT: D 240 MET cc_start: 0.8750 (mmm) cc_final: 0.8367 (mmm) REVERT: D 277 ASP cc_start: 0.7669 (t0) cc_final: 0.7388 (t0) outliers start: 10 outliers final: 6 residues processed: 125 average time/residue: 0.2983 time to fit residues: 48.4984 Evaluate side-chains 111 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN C 306 GLN C 474 GLN C 541 GLN C 553 GLN D 143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.088468 restraints weight = 11190.453| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.51 r_work: 0.2794 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9269 Z= 0.335 Angle : 0.611 7.569 12604 Z= 0.306 Chirality : 0.043 0.178 1461 Planarity : 0.004 0.046 1604 Dihedral : 8.680 73.248 1329 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.59 % Allowed : 8.70 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1157 helix: 1.28 (0.19), residues: 721 sheet: 0.17 (0.63), residues: 59 loop : -0.46 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 81 HIS 0.004 0.001 HIS C 424 PHE 0.018 0.002 PHE D 467 TYR 0.017 0.002 TYR D 88 ARG 0.005 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.105 Fit side-chains REVERT: C 183 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7834 (ttp-110) REVERT: C 515 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7456 (tm-30) REVERT: D 1 MET cc_start: 0.5946 (ptt) cc_final: 0.5273 (tpt) REVERT: D 154 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8699 (mt) REVERT: D 167 LEU cc_start: 0.8915 (tp) cc_final: 0.8628 (tp) REVERT: D 277 ASP cc_start: 0.7713 (t0) cc_final: 0.7336 (t0) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.2740 time to fit residues: 43.9247 Evaluate side-chains 119 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.091273 restraints weight = 10980.230| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.49 r_work: 0.2850 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9269 Z= 0.198 Angle : 0.523 6.640 12604 Z= 0.266 Chirality : 0.040 0.145 1461 Planarity : 0.004 0.043 1604 Dihedral : 7.266 73.895 1329 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.48 % Allowed : 9.97 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.25), residues: 1157 helix: 1.69 (0.19), residues: 722 sheet: 0.06 (0.63), residues: 59 loop : -0.41 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.013 0.001 PHE D 467 TYR 0.018 0.001 TYR D 88 ARG 0.004 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.954 Fit side-chains REVERT: C 515 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7429 (tm-30) REVERT: D 1 MET cc_start: 0.5820 (ptt) cc_final: 0.5232 (tpt) REVERT: D 11 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7743 (ttt180) REVERT: D 14 LYS cc_start: 0.8546 (tttt) cc_final: 0.7640 (tptt) REVERT: D 15 GLN cc_start: 0.8477 (mt0) cc_final: 0.7963 (tp-100) REVERT: D 167 LEU cc_start: 0.8895 (tp) cc_final: 0.8588 (tp) REVERT: D 207 ASP cc_start: 0.8200 (t0) cc_final: 0.7879 (t0) REVERT: D 277 ASP cc_start: 0.7716 (t0) cc_final: 0.7397 (t0) outliers start: 14 outliers final: 10 residues processed: 119 average time/residue: 0.2753 time to fit residues: 43.2337 Evaluate side-chains 115 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 482 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.091086 restraints weight = 11003.109| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.51 r_work: 0.2828 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9269 Z= 0.206 Angle : 0.518 7.055 12604 Z= 0.262 Chirality : 0.040 0.150 1461 Planarity : 0.004 0.042 1604 Dihedral : 6.736 73.221 1329 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.01 % Allowed : 10.29 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1157 helix: 1.87 (0.20), residues: 722 sheet: 0.05 (0.64), residues: 59 loop : -0.36 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.014 0.001 PHE D 467 TYR 0.018 0.001 TYR D 88 ARG 0.003 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.945 Fit side-chains REVERT: C 515 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7482 (tm-30) REVERT: D 1 MET cc_start: 0.5789 (ptt) cc_final: 0.5224 (tpt) REVERT: D 11 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7740 (ttt180) REVERT: D 207 ASP cc_start: 0.8222 (t0) cc_final: 0.7884 (t0) outliers start: 19 outliers final: 14 residues processed: 118 average time/residue: 0.2797 time to fit residues: 43.2148 Evaluate side-chains 117 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.114143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.091835 restraints weight = 10953.393| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.50 r_work: 0.2839 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9269 Z= 0.188 Angle : 0.498 7.097 12604 Z= 0.254 Chirality : 0.039 0.156 1461 Planarity : 0.004 0.043 1604 Dihedral : 6.426 72.350 1329 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.91 % Allowed : 11.03 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.25), residues: 1157 helix: 1.99 (0.19), residues: 723 sheet: 0.12 (0.65), residues: 59 loop : -0.31 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 427 HIS 0.003 0.001 HIS C 85 PHE 0.013 0.001 PHE D 467 TYR 0.018 0.001 TYR D 88 ARG 0.004 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.963 Fit side-chains REVERT: C 515 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7477 (tm-30) REVERT: D 1 MET cc_start: 0.5751 (ptt) cc_final: 0.5148 (tpt) REVERT: D 11 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7705 (ttt180) REVERT: D 207 ASP cc_start: 0.8201 (t0) cc_final: 0.7873 (t0) REVERT: D 216 ARG cc_start: 0.8498 (ttp-170) cc_final: 0.8169 (ptt90) outliers start: 18 outliers final: 14 residues processed: 120 average time/residue: 0.2847 time to fit residues: 44.7294 Evaluate side-chains 117 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 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 = 0.3210 r_free = 0.3210 target = 0.114406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.092100 restraints weight = 11066.003| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.50 r_work: 0.2865 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9269 Z= 0.186 Angle : 0.500 7.142 12604 Z= 0.254 Chirality : 0.039 0.145 1461 Planarity : 0.004 0.044 1604 Dihedral : 6.308 71.474 1329 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.91 % Allowed : 11.24 % Favored : 86.85 % 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: 1.85 (0.25), residues: 1157 helix: 2.10 (0.19), residues: 723 sheet: 0.15 (0.66), residues: 59 loop : -0.28 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.013 0.001 PHE D 467 TYR 0.018 0.001 TYR D 88 ARG 0.003 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.020 Fit side-chains REVERT: D 1 MET cc_start: 0.5763 (ptt) cc_final: 0.5162 (tpt) REVERT: D 11 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7787 (ttt180) REVERT: D 207 ASP cc_start: 0.8178 (t0) cc_final: 0.7879 (t0) REVERT: D 216 ARG cc_start: 0.8515 (ttp-170) cc_final: 0.8211 (ptt90) outliers start: 18 outliers final: 16 residues processed: 117 average time/residue: 0.3066 time to fit residues: 47.1986 Evaluate side-chains 120 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.114267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.091777 restraints weight = 11208.306| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.51 r_work: 0.2807 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9269 Z= 0.199 Angle : 0.504 7.410 12604 Z= 0.256 Chirality : 0.040 0.146 1461 Planarity : 0.004 0.043 1604 Dihedral : 6.241 70.967 1329 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.80 % Allowed : 11.98 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.25), residues: 1157 helix: 2.13 (0.19), residues: 723 sheet: 0.14 (0.66), residues: 59 loop : -0.30 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 PHE 0.013 0.001 PHE D 467 TYR 0.018 0.001 TYR D 88 ARG 0.003 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.104 Fit side-chains REVERT: D 1 MET cc_start: 0.5797 (ptt) cc_final: 0.5183 (tpt) REVERT: D 11 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7731 (ttt180) REVERT: D 207 ASP cc_start: 0.8183 (t0) cc_final: 0.7859 (t0) REVERT: D 216 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8184 (ptt90) REVERT: D 585 GLN cc_start: 0.7465 (mt0) cc_final: 0.7180 (mm110) outliers start: 17 outliers final: 16 residues processed: 117 average time/residue: 0.3593 time to fit residues: 55.9881 Evaluate side-chains 120 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 541 GLN D 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.093003 restraints weight = 10981.048| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.50 r_work: 0.2902 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9269 Z= 0.167 Angle : 0.487 7.601 12604 Z= 0.248 Chirality : 0.039 0.143 1461 Planarity : 0.004 0.044 1604 Dihedral : 6.101 68.949 1329 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.91 % Allowed : 11.88 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.25), residues: 1157 helix: 2.25 (0.19), residues: 722 sheet: 0.20 (0.66), residues: 59 loop : -0.27 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 81 HIS 0.004 0.001 HIS C 85 PHE 0.012 0.001 PHE D 467 TYR 0.018 0.001 TYR D 88 ARG 0.003 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.072 Fit side-chains REVERT: D 1 MET cc_start: 0.5716 (ptt) cc_final: 0.5153 (tpt) REVERT: D 11 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7855 (ttt180) REVERT: D 207 ASP cc_start: 0.8153 (t0) cc_final: 0.7880 (t0) REVERT: D 216 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.8202 (ptt90) REVERT: D 526 GLU cc_start: 0.8326 (tt0) cc_final: 0.7950 (mt-10) REVERT: D 585 GLN cc_start: 0.7474 (mt0) cc_final: 0.7197 (mm110) outliers start: 18 outliers final: 16 residues processed: 123 average time/residue: 0.2872 time to fit residues: 46.6500 Evaluate side-chains 122 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 0.0000 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.0070 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 HIS C 531 HIS D 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.116883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.094626 restraints weight = 11031.114| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.50 r_work: 0.2853 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9269 Z= 0.147 Angle : 0.481 8.421 12604 Z= 0.244 Chirality : 0.038 0.142 1461 Planarity : 0.003 0.045 1604 Dihedral : 5.892 64.920 1329 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.91 % Allowed : 11.88 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.25), residues: 1157 helix: 2.37 (0.19), residues: 722 sheet: 0.29 (0.67), residues: 59 loop : -0.25 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 81 HIS 0.004 0.000 HIS C 85 PHE 0.011 0.001 PHE D 467 TYR 0.017 0.001 TYR D 88 ARG 0.004 0.000 ARG D 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.957 Fit side-chains REVERT: D 1 MET cc_start: 0.5670 (ptt) cc_final: 0.5111 (tpt) REVERT: D 11 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7871 (ttm-80) REVERT: D 108 GLN cc_start: 0.8153 (tt0) cc_final: 0.7922 (mt0) REVERT: D 526 GLU cc_start: 0.8299 (tt0) cc_final: 0.7937 (mt-10) REVERT: D 585 GLN cc_start: 0.7392 (mt0) cc_final: 0.7126 (mm110) outliers start: 18 outliers final: 14 residues processed: 122 average time/residue: 0.2860 time to fit residues: 46.3076 Evaluate side-chains 119 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 17 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 531 HIS D 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.116905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.094565 restraints weight = 10959.618| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.50 r_work: 0.2870 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9269 Z= 0.170 Angle : 0.502 8.052 12604 Z= 0.251 Chirality : 0.039 0.145 1461 Planarity : 0.004 0.044 1604 Dihedral : 5.871 64.223 1329 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.70 % Allowed : 11.98 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.25), residues: 1157 helix: 2.36 (0.19), residues: 722 sheet: 0.27 (0.67), residues: 59 loop : -0.21 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 81 HIS 0.004 0.001 HIS C 85 PHE 0.012 0.001 PHE D 467 TYR 0.018 0.001 TYR D 88 ARG 0.003 0.000 ARG D 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4999.34 seconds wall clock time: 87 minutes 53.19 seconds (5273.19 seconds total)