Starting phenix.real_space_refine on Tue Mar 3 22:05:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zd5_14636/03_2026/7zd5_14636_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zd5_14636/03_2026/7zd5_14636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zd5_14636/03_2026/7zd5_14636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zd5_14636/03_2026/7zd5_14636.map" model { file = "/net/cci-nas-00/data/ceres_data/7zd5_14636/03_2026/7zd5_14636_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zd5_14636/03_2026/7zd5_14636_neut.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 5750 2.51 5 N 1575 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8967 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4383 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 551} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 4584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4584 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 27, 'TRANS': 559} Time building chain proxies: 2.43, per 1000 atoms: 0.27 Number of scatterers: 8967 At special positions: 0 Unit cell: (115.506, 95.418, 112.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1613 8.00 N 1575 7.00 C 5750 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: 0.77 Conformation dependent library (CDL) restraints added in 386.1 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 67.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 13 removed outlier: 3.854A pdb=" N ARG C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 14 through 50 removed outlier: 3.657A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 54 Processing helix chain 'C' and resid 61 through 103 removed outlier: 3.759A pdb=" N ARG C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.979A pdb=" N GLN C 116 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'C' and resid 131 through 137 removed outlier: 4.518A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 157 removed outlier: 3.854A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 176 Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 185 through 208 removed outlier: 3.600A pdb=" N GLY C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 220 through 267 removed outlier: 3.664A pdb=" N THR C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 244 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 3.548A 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 296 through 318 removed outlier: 3.754A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 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 removed outlier: 3.903A pdb=" N GLN C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 476 through 492 Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.959A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 555 through 562 removed outlier: 3.645A pdb=" N ARG C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 571 removed outlier: 3.640A pdb=" N GLN C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 21 through 54 removed outlier: 3.613A pdb=" N ARG D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 109 removed outlier: 3.589A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 139 removed outlier: 3.588A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 162 removed outlier: 3.667A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.668A 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 164 through 183 removed outlier: 3.627A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix Processing helix chain 'D' and resid 183 through 194 removed outlier: 3.618A pdb=" N ASN D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 211 through 218 removed outlier: 3.564A pdb=" N PHE D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 273 removed outlier: 4.069A pdb=" N GLU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 310 Proline residue: D 298 - end of helix removed outlier: 3.921A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 311 through 328 removed outlier: 3.822A pdb=" N THR D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 398 removed outlier: 3.955A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.519A pdb=" N VAL D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.823A pdb=" N ASP D 476 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 500 removed outlier: 3.731A pdb=" N ARG D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 535 removed outlier: 3.870A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 533 " --> pdb=" O ASN D 529 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 550 removed outlier: 4.168A pdb=" N ASP D 549 " --> pdb=" O ASP D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.989A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 587 removed outlier: 3.541A pdb=" N GLU D 587 " --> pdb=" O HIS D 583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 339 through 342 Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.462A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR C 530 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE C 371 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 428 through 429 Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.462A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 425 through 429 removed outlier: 6.932A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ASP D 510 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D 428 " --> pdb=" O ASP D 510 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET D 539 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY D 383 " --> pdb=" O THR D 541 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N TRP D 554 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL D 380 " --> pdb=" O TRP D 554 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET D 556 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.07 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: 1866 1.33 - 1.45: 2024 1.45 - 1.57: 5198 1.57 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 9143 Sorted by residual: bond pdb=" N ASN D 431 " pdb=" CA ASN D 431 " ideal model delta sigma weight residual 1.457 1.488 -0.032 9.10e-03 1.21e+04 1.22e+01 bond pdb=" N LEU C 533 " pdb=" CA LEU C 533 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.08e-02 8.57e+03 9.17e+00 bond pdb=" N GLN D 430 " pdb=" CA GLN D 430 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.34e-02 5.57e+03 7.91e+00 bond pdb=" N GLN D 302 " pdb=" CA GLN D 302 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.04e-02 9.25e+03 7.39e+00 bond pdb=" C ALA D 90 " pdb=" O ALA D 90 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.16e-02 7.43e+03 7.21e+00 ... (remaining 9138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12065 1.90 - 3.81: 297 3.81 - 5.71: 49 5.71 - 7.61: 7 7.61 - 9.51: 3 Bond angle restraints: 12421 Sorted by residual: angle pdb=" C GLU C 118 " pdb=" N LEU C 119 " pdb=" CA LEU C 119 " ideal model delta sigma weight residual 120.44 129.95 -9.51 1.36e+00 5.41e-01 4.89e+01 angle pdb=" N GLU C 118 " pdb=" CA GLU C 118 " pdb=" C GLU C 118 " ideal model delta sigma weight residual 113.17 104.45 8.72 1.26e+00 6.30e-01 4.79e+01 angle pdb=" N ILE D 19 " pdb=" CA ILE D 19 " pdb=" C ILE D 19 " ideal model delta sigma weight residual 109.30 102.95 6.35 1.25e+00 6.40e-01 2.58e+01 angle pdb=" CA GLU C 118 " pdb=" C GLU C 118 " pdb=" N LEU C 119 " ideal model delta sigma weight residual 118.27 112.69 5.58 1.31e+00 5.83e-01 1.82e+01 angle pdb=" C ASN D 431 " pdb=" CA ASN D 431 " pdb=" CB ASN D 431 " ideal model delta sigma weight residual 110.71 114.59 -3.88 9.40e-01 1.13e+00 1.71e+01 ... (remaining 12416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 4853 16.91 - 33.82: 484 33.82 - 50.73: 106 50.73 - 67.64: 10 67.64 - 84.55: 6 Dihedral angle restraints: 5459 sinusoidal: 2142 harmonic: 3317 Sorted by residual: dihedral pdb=" CA THR D 541 " pdb=" C THR D 541 " pdb=" N HIS D 542 " pdb=" CA HIS D 542 " ideal model delta harmonic sigma weight residual 180.00 160.77 19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PRO C 296 " pdb=" C PRO C 296 " pdb=" N VAL C 297 " pdb=" CA VAL C 297 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" C HIS D 93 " pdb=" N HIS D 93 " pdb=" CA HIS D 93 " pdb=" CB HIS D 93 " ideal model delta harmonic sigma weight residual -122.60 -131.27 8.67 0 2.50e+00 1.60e-01 1.20e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1216 0.058 - 0.116: 203 0.116 - 0.174: 22 0.174 - 0.232: 6 0.232 - 0.289: 2 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CA ILE D 19 " pdb=" N ILE D 19 " pdb=" C ILE D 19 " pdb=" CB ILE D 19 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA HIS D 93 " pdb=" N HIS D 93 " pdb=" C HIS D 93 " pdb=" CB HIS D 93 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ARG C 2 " pdb=" N ARG C 2 " pdb=" C ARG C 2 " pdb=" CB ARG C 2 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1446 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 90 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C ALA D 90 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA D 90 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY D 91 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 557 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C GLN D 557 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN D 557 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP D 558 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 89 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C HIS D 89 " -0.036 2.00e-02 2.50e+03 pdb=" O HIS D 89 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA D 90 " 0.012 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1421 2.76 - 3.29: 8859 3.29 - 3.83: 14276 3.83 - 4.36: 17801 4.36 - 4.90: 30676 Nonbonded interactions: 73033 Sorted by model distance: nonbonded pdb=" NH2 ARG D 105 " pdb=" O THR D 330 " model vdw 2.219 3.120 nonbonded pdb=" ND2 ASN D 162 " pdb=" OH TYR D 267 " model vdw 2.229 3.120 nonbonded pdb=" NE2 GLN C 421 " pdb=" OE1 GLU C 500 " model vdw 2.230 3.120 nonbonded pdb=" O ALA C 365 " pdb=" OG1 THR C 525 " model vdw 2.249 3.040 nonbonded pdb=" O SER C 315 " pdb=" CB ASP C 319 " model vdw 2.262 3.440 ... (remaining 73028 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: 2.350 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.050 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 9143 Z= 0.304 Angle : 0.725 9.515 12421 Z= 0.449 Chirality : 0.047 0.289 1449 Planarity : 0.004 0.041 1590 Dihedral : 13.880 84.554 3319 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.11 % Allowed : 1.60 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.23), residues: 1151 helix: -1.55 (0.18), residues: 683 sheet: -0.66 (0.75), residues: 49 loop : -0.40 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 452 TYR 0.011 0.001 TYR D 88 PHE 0.012 0.001 PHE C 216 TRP 0.023 0.001 TRP D 427 HIS 0.004 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 9143) covalent geometry : angle 0.72502 (12421) hydrogen bonds : bond 0.26685 ( 521) hydrogen bonds : angle 9.51280 ( 1521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: C 12 LYS cc_start: 0.8533 (tttt) cc_final: 0.8149 (mmtm) REVERT: C 262 MET cc_start: 0.8726 (mmp) cc_final: 0.8499 (mmp) REVERT: C 520 MET cc_start: 0.7007 (mtm) cc_final: 0.6756 (mtm) REVERT: D 19 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7694 (tp) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1286 time to fit residues: 14.9924 Evaluate side-chains 72 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 GLN C 571 GLN D 41 GLN D 92 GLN D 93 HIS D 129 GLN D 377 GLN D 431 ASN D 490 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.090968 restraints weight = 11230.251| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.76 r_work: 0.2899 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9143 Z= 0.146 Angle : 0.602 6.084 12421 Z= 0.308 Chirality : 0.040 0.149 1449 Planarity : 0.005 0.038 1590 Dihedral : 4.401 17.707 1259 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.86 % Allowed : 7.38 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1151 helix: 0.17 (0.19), residues: 692 sheet: -0.22 (0.79), residues: 49 loop : -0.50 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 522 TYR 0.019 0.001 TYR D 88 PHE 0.014 0.001 PHE C 346 TRP 0.023 0.002 TRP D 427 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9143) covalent geometry : angle 0.60217 (12421) hydrogen bonds : bond 0.05409 ( 521) hydrogen bonds : angle 4.84800 ( 1521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.325 Fit side-chains REVERT: C 12 LYS cc_start: 0.8744 (tttt) cc_final: 0.7903 (mmtm) REVERT: C 183 ARG cc_start: 0.8542 (ttp80) cc_final: 0.7832 (mtm110) REVERT: C 319 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: C 515 GLU cc_start: 0.8351 (mp0) cc_final: 0.7795 (mp0) REVERT: D 71 LEU cc_start: 0.8720 (tp) cc_final: 0.8402 (mt) REVERT: D 154 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8007 (mp) REVERT: D 525 MET cc_start: 0.8379 (mmt) cc_final: 0.7907 (mmt) outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 0.1058 time to fit residues: 14.4934 Evaluate side-chains 88 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 154 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 0.0070 chunk 46 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.129044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.092636 restraints weight = 11233.641| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.76 r_work: 0.2945 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9143 Z= 0.119 Angle : 0.529 6.803 12421 Z= 0.269 Chirality : 0.039 0.141 1449 Planarity : 0.003 0.036 1590 Dihedral : 4.060 16.734 1257 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.96 % Allowed : 10.91 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1151 helix: 1.05 (0.20), residues: 700 sheet: -0.02 (0.77), residues: 49 loop : -0.42 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 384 TYR 0.018 0.001 TYR D 88 PHE 0.011 0.001 PHE C 164 TRP 0.016 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9143) covalent geometry : angle 0.52939 (12421) hydrogen bonds : bond 0.04522 ( 521) hydrogen bonds : angle 4.28401 ( 1521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.311 Fit side-chains REVERT: C 12 LYS cc_start: 0.8720 (tttt) cc_final: 0.7928 (mmtm) REVERT: C 183 ARG cc_start: 0.8550 (ttp80) cc_final: 0.7849 (mtm110) REVERT: D 71 LEU cc_start: 0.8707 (tp) cc_final: 0.8405 (mt) REVERT: D 154 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8166 (mp) REVERT: D 441 ASP cc_start: 0.8308 (t0) cc_final: 0.8009 (t0) REVERT: D 525 MET cc_start: 0.8388 (mmt) cc_final: 0.7921 (mmt) outliers start: 9 outliers final: 4 residues processed: 106 average time/residue: 0.1070 time to fit residues: 15.1772 Evaluate side-chains 88 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 62 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN C 571 GLN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.093749 restraints weight = 11242.885| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.77 r_work: 0.2945 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9143 Z= 0.121 Angle : 0.533 12.735 12421 Z= 0.265 Chirality : 0.039 0.132 1449 Planarity : 0.003 0.037 1590 Dihedral : 3.949 17.331 1257 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.28 % Allowed : 11.87 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1151 helix: 1.41 (0.20), residues: 701 sheet: 0.13 (0.78), residues: 49 loop : -0.34 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.017 0.001 TYR D 88 PHE 0.010 0.001 PHE C 216 TRP 0.017 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9143) covalent geometry : angle 0.53272 (12421) hydrogen bonds : bond 0.04210 ( 521) hydrogen bonds : angle 4.09271 ( 1521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.220 Fit side-chains REVERT: C 12 LYS cc_start: 0.8723 (tttt) cc_final: 0.7964 (mmtm) REVERT: C 183 ARG cc_start: 0.8543 (ttp80) cc_final: 0.7828 (mtm110) REVERT: C 212 GLU cc_start: 0.7843 (mp0) cc_final: 0.7612 (mp0) REVERT: C 367 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8017 (mt-10) REVERT: D 71 LEU cc_start: 0.8703 (tp) cc_final: 0.8427 (mt) REVERT: D 154 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8219 (mp) REVERT: D 427 TRP cc_start: 0.7299 (p-90) cc_final: 0.7040 (p-90) REVERT: D 441 ASP cc_start: 0.8267 (t0) cc_final: 0.7989 (t0) REVERT: D 525 MET cc_start: 0.8360 (mmt) cc_final: 0.7916 (mmt) REVERT: D 570 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7406 (tt) outliers start: 12 outliers final: 6 residues processed: 100 average time/residue: 0.1085 time to fit residues: 14.4781 Evaluate side-chains 93 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 546 ASP Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN C 571 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.128904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.094501 restraints weight = 11222.985| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.64 r_work: 0.2937 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9143 Z= 0.127 Angle : 0.530 11.145 12421 Z= 0.264 Chirality : 0.039 0.132 1449 Planarity : 0.003 0.038 1590 Dihedral : 3.878 17.187 1257 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.71 % Allowed : 13.16 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.25), residues: 1151 helix: 1.61 (0.20), residues: 701 sheet: 0.22 (0.78), residues: 49 loop : -0.30 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.017 0.001 TYR D 88 PHE 0.011 0.001 PHE C 216 TRP 0.017 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9143) covalent geometry : angle 0.52979 (12421) hydrogen bonds : bond 0.04116 ( 521) hydrogen bonds : angle 3.99473 ( 1521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.348 Fit side-chains REVERT: C 12 LYS cc_start: 0.8662 (tttt) cc_final: 0.7897 (mmtm) REVERT: C 183 ARG cc_start: 0.8483 (ttp80) cc_final: 0.7773 (mtm110) REVERT: C 367 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8029 (mt-10) REVERT: C 520 MET cc_start: 0.8223 (mmm) cc_final: 0.7969 (mmt) REVERT: D 71 LEU cc_start: 0.8678 (tp) cc_final: 0.8387 (mt) REVERT: D 154 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8157 (mp) REVERT: D 427 TRP cc_start: 0.7240 (p-90) cc_final: 0.6988 (p-90) REVERT: D 441 ASP cc_start: 0.8240 (t0) cc_final: 0.8006 (m-30) REVERT: D 525 MET cc_start: 0.8341 (mmt) cc_final: 0.7872 (mmt) REVERT: D 570 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7380 (tt) outliers start: 16 outliers final: 9 residues processed: 106 average time/residue: 0.1051 time to fit residues: 15.0222 Evaluate side-chains 97 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 546 ASP Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.090931 restraints weight = 11242.368| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.77 r_work: 0.2907 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9143 Z= 0.150 Angle : 0.549 10.174 12421 Z= 0.271 Chirality : 0.040 0.151 1449 Planarity : 0.004 0.035 1590 Dihedral : 3.905 17.645 1257 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.60 % Allowed : 14.65 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.25), residues: 1151 helix: 1.58 (0.20), residues: 704 sheet: 0.17 (0.78), residues: 49 loop : -0.20 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.017 0.001 TYR D 88 PHE 0.013 0.001 PHE C 216 TRP 0.016 0.001 TRP D 81 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9143) covalent geometry : angle 0.54861 (12421) hydrogen bonds : bond 0.04236 ( 521) hydrogen bonds : angle 3.99140 ( 1521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.256 Fit side-chains REVERT: C 12 LYS cc_start: 0.8712 (tttt) cc_final: 0.7951 (mmtm) REVERT: C 183 ARG cc_start: 0.8530 (ttp80) cc_final: 0.7810 (mtm110) REVERT: C 367 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8078 (mt-10) REVERT: D 71 LEU cc_start: 0.8646 (tp) cc_final: 0.8414 (mt) REVERT: D 154 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8215 (mp) REVERT: D 441 ASP cc_start: 0.8275 (t0) cc_final: 0.8048 (m-30) REVERT: D 525 MET cc_start: 0.8322 (mmt) cc_final: 0.7892 (mmt) REVERT: D 570 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7435 (tt) REVERT: D 588 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7385 (pt) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 0.0905 time to fit residues: 12.6810 Evaluate side-chains 98 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 546 ASP Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 588 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.093626 restraints weight = 11288.245| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.64 r_work: 0.2925 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9143 Z= 0.136 Angle : 0.538 9.540 12421 Z= 0.267 Chirality : 0.040 0.130 1449 Planarity : 0.003 0.037 1590 Dihedral : 3.878 17.632 1257 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.14 % Allowed : 14.22 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.25), residues: 1151 helix: 1.68 (0.20), residues: 704 sheet: 0.39 (0.76), residues: 55 loop : -0.15 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.017 0.001 TYR D 88 PHE 0.013 0.001 PHE C 216 TRP 0.017 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9143) covalent geometry : angle 0.53813 (12421) hydrogen bonds : bond 0.04122 ( 521) hydrogen bonds : angle 3.94415 ( 1521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.230 Fit side-chains REVERT: C 12 LYS cc_start: 0.8670 (tttt) cc_final: 0.7905 (mmtm) REVERT: C 183 ARG cc_start: 0.8480 (ttp80) cc_final: 0.7761 (mtm110) REVERT: C 367 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8026 (mt-10) REVERT: D 71 LEU cc_start: 0.8600 (tp) cc_final: 0.8364 (mt) REVERT: D 154 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8158 (mp) REVERT: D 201 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8428 (mp) REVERT: D 441 ASP cc_start: 0.8256 (t0) cc_final: 0.8039 (m-30) REVERT: D 525 MET cc_start: 0.8237 (mmt) cc_final: 0.7847 (mmt) REVERT: D 570 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7365 (tt) REVERT: D 588 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7332 (pt) outliers start: 20 outliers final: 8 residues processed: 108 average time/residue: 0.0992 time to fit residues: 14.7901 Evaluate side-chains 103 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 588 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN ** D 442 ASN ** 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 = 0.3432 r_free = 0.3432 target = 0.127636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.090815 restraints weight = 11281.991| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.77 r_work: 0.2799 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9143 Z= 0.152 Angle : 0.556 9.173 12421 Z= 0.275 Chirality : 0.040 0.143 1449 Planarity : 0.004 0.037 1590 Dihedral : 3.901 17.626 1257 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.71 % Allowed : 14.55 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.25), residues: 1151 helix: 1.66 (0.20), residues: 704 sheet: 0.32 (0.75), residues: 55 loop : -0.16 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.017 0.001 TYR D 88 PHE 0.014 0.001 PHE C 216 TRP 0.017 0.001 TRP D 81 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9143) covalent geometry : angle 0.55551 (12421) hydrogen bonds : bond 0.04201 ( 521) hydrogen bonds : angle 3.95824 ( 1521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.330 Fit side-chains REVERT: C 12 LYS cc_start: 0.8673 (tttt) cc_final: 0.7854 (mmtm) REVERT: C 183 ARG cc_start: 0.8492 (ttp80) cc_final: 0.7761 (mtm110) REVERT: C 367 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8069 (mt-10) REVERT: C 514 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8075 (mm) REVERT: C 515 GLU cc_start: 0.7849 (pp20) cc_final: 0.7529 (mp0) REVERT: D 71 LEU cc_start: 0.8552 (tp) cc_final: 0.8308 (mt) REVERT: D 154 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8055 (mp) REVERT: D 201 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8405 (mp) REVERT: D 441 ASP cc_start: 0.8316 (t0) cc_final: 0.8105 (m-30) REVERT: D 525 MET cc_start: 0.8180 (mmt) cc_final: 0.7780 (mmt) REVERT: D 570 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7312 (tt) REVERT: D 588 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7248 (pt) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.1060 time to fit residues: 14.4590 Evaluate side-chains 101 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 588 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 chunk 77 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN ** D 442 ASN ** 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 = 0.3467 r_free = 0.3467 target = 0.130273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.093533 restraints weight = 11173.801| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.79 r_work: 0.2828 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9143 Z= 0.117 Angle : 0.531 8.704 12421 Z= 0.262 Chirality : 0.039 0.129 1449 Planarity : 0.003 0.040 1590 Dihedral : 3.796 16.835 1257 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.71 % Allowed : 14.87 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.25), residues: 1151 helix: 1.88 (0.20), residues: 703 sheet: 0.36 (0.75), residues: 55 loop : -0.11 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.018 0.001 TYR D 88 PHE 0.011 0.001 PHE C 216 TRP 0.018 0.001 TRP D 81 HIS 0.003 0.000 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9143) covalent geometry : angle 0.53144 (12421) hydrogen bonds : bond 0.03917 ( 521) hydrogen bonds : angle 3.85102 ( 1521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.307 Fit side-chains REVERT: C 12 LYS cc_start: 0.8657 (tttt) cc_final: 0.7863 (mmtm) REVERT: C 183 ARG cc_start: 0.8488 (ttp80) cc_final: 0.7787 (mtm110) REVERT: C 367 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8074 (mt-10) REVERT: D 11 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7838 (ttm110) REVERT: D 71 LEU cc_start: 0.8554 (tp) cc_final: 0.8334 (mt) REVERT: D 154 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8110 (mp) REVERT: D 201 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8377 (mp) REVERT: D 441 ASP cc_start: 0.8295 (t0) cc_final: 0.8088 (m-30) REVERT: D 525 MET cc_start: 0.8172 (mmt) cc_final: 0.7774 (mmt) REVERT: D 570 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7285 (tt) outliers start: 16 outliers final: 9 residues processed: 108 average time/residue: 0.1133 time to fit residues: 16.4366 Evaluate side-chains 100 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.094272 restraints weight = 11155.375| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.77 r_work: 0.2839 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9143 Z= 0.111 Angle : 0.549 14.729 12421 Z= 0.268 Chirality : 0.039 0.199 1449 Planarity : 0.004 0.045 1590 Dihedral : 3.768 16.734 1257 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.28 % Allowed : 15.51 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1151 helix: 1.98 (0.20), residues: 703 sheet: 0.34 (0.75), residues: 55 loop : -0.10 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 193 TYR 0.017 0.001 TYR D 88 PHE 0.010 0.001 PHE C 216 TRP 0.018 0.001 TRP D 81 HIS 0.003 0.000 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9143) covalent geometry : angle 0.54857 (12421) hydrogen bonds : bond 0.03818 ( 521) hydrogen bonds : angle 3.82749 ( 1521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: C 12 LYS cc_start: 0.8619 (tttt) cc_final: 0.7812 (mmtm) REVERT: C 183 ARG cc_start: 0.8443 (ttp80) cc_final: 0.7746 (mtm110) REVERT: C 367 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8061 (mt-10) REVERT: D 11 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7809 (ttm110) REVERT: D 71 LEU cc_start: 0.8522 (tp) cc_final: 0.8257 (mt) REVERT: D 154 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8096 (mp) REVERT: D 193 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7684 (mtm-85) REVERT: D 201 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8339 (mp) REVERT: D 441 ASP cc_start: 0.8278 (t0) cc_final: 0.8061 (m-30) REVERT: D 525 MET cc_start: 0.8119 (mmt) cc_final: 0.7725 (mmt) REVERT: D 570 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7286 (tt) outliers start: 12 outliers final: 6 residues processed: 107 average time/residue: 0.1087 time to fit residues: 15.7215 Evaluate side-chains 99 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.094136 restraints weight = 11084.448| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.76 r_work: 0.2828 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9143 Z= 0.122 Angle : 0.552 14.390 12421 Z= 0.269 Chirality : 0.039 0.175 1449 Planarity : 0.004 0.047 1590 Dihedral : 3.759 16.495 1257 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.07 % Allowed : 15.72 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1151 helix: 1.96 (0.20), residues: 704 sheet: 0.41 (0.75), residues: 55 loop : -0.09 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 193 TYR 0.017 0.001 TYR D 88 PHE 0.012 0.001 PHE C 216 TRP 0.018 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9143) covalent geometry : angle 0.55237 (12421) hydrogen bonds : bond 0.03909 ( 521) hydrogen bonds : angle 3.82412 ( 1521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.33 seconds wall clock time: 38 minutes 51.77 seconds (2331.77 seconds total)