Starting phenix.real_space_refine on Thu Jul 2 13:07:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5r_61150/07_2026/9j5r_61150.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5r_61150/07_2026/9j5r_61150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j5r_61150/07_2026/9j5r_61150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5r_61150/07_2026/9j5r_61150.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5r_61150/07_2026/9j5r_61150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5r_61150/07_2026/9j5r_61150.cif" } resolution = 4.3 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= 0.001 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 2 7.51 5 S 36 5.16 5 C 5397 2.51 5 N 1481 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8542 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3789 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 28, 'TRANS': 503} Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 11, 'ASN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 3, 'ARG:plan': 10, 'HIS:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 229 Chain: "B" Number of atoms: 2727 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 387, 2717 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 5 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 491 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'PHE:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 5, 'GLN:plan1': 5, 'HIS:plan': 2, 'ARG:plan': 1, 'GLU:plan': 15} Unresolved non-hydrogen planarities: 205 Conformer: "B" Number of residues, atoms: 387, 2717 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 5 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 491 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'PHE:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 5, 'GLN:plan1': 5, 'HIS:plan': 2, 'ARG:plan': 1, 'GLU:plan': 15} Unresolved non-hydrogen planarities: 205 bond proxies already assigned to first conformer: 2752 Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2024 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 135 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS B 312 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS B 312 " occ=0.50 residue: pdb=" N AASN B 471 " occ=0.50 ... (8 atoms not shown) pdb=" CB BASN B 471 " occ=0.50 Time building chain proxies: 2.05, per 1000 atoms: 0.24 Number of scatterers: 8542 At special positions: 0 Unit cell: (89.04, 126.14, 130.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 2 24.99 S 36 16.00 O 1626 8.00 N 1481 7.00 C 5397 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: 0.56 Conformation dependent library (CDL) restraints added in 264.3 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 1 sheets defined 75.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 61 through 78 removed outlier: 3.758A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 80 through 98 removed outlier: 3.892A pdb=" N ALA A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.763A pdb=" N ARG A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 137 removed outlier: 3.728A pdb=" N HIS A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.960A pdb=" N VAL A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.719A pdb=" N ARG A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 removed outlier: 3.656A pdb=" N LYS A 200 " --> pdb=" O ALA A 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 201 through 212 Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.946A pdb=" N LEU A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 256 through 270 Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.898A pdb=" N LEU A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.964A pdb=" N ALA A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 332 through 346 removed outlier: 3.573A pdb=" N SER A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.683A pdb=" N GLU A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Proline residue: A 361 - end of helix removed outlier: 3.635A pdb=" N ASP A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 381 removed outlier: 3.788A pdb=" N ARG A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 removed outlier: 4.504A pdb=" N VAL A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 407 Proline residue: A 400 - end of helix Processing helix chain 'A' and resid 410 through 425 removed outlier: 3.968A pdb=" N TYR A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Proline residue: A 422 - end of helix Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'A' and resid 449 through 467 Processing helix chain 'A' and resid 468 through 486 Proline residue: A 478 - end of helix removed outlier: 3.684A pdb=" N ASN A 486 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.864A pdb=" N ARG A 492 " --> pdb=" O HIS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 507 through 514 Processing helix chain 'A' and resid 514 through 524 removed outlier: 4.280A pdb=" N VAL A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 542 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 546 through 563 Proline residue: A 556 - end of helix removed outlier: 3.518A pdb=" N SER A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 581 Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 201 through 217 removed outlier: 4.052A pdb=" N ALA B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.739A pdb=" N THR B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 250 through 268 removed outlier: 3.668A pdb=" N LYS B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 280 removed outlier: 4.183A pdb=" N ASP B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.809A pdb=" N ASN B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 324 through 338 Proline residue: B 330 - end of helix removed outlier: 3.929A pdb=" N VAL B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 359 Processing helix chain 'B' and resid 362 through 370 Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.561A pdb=" N ALA B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 398 removed outlier: 4.068A pdb=" N THR B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 417 through 430 Processing helix chain 'B' and resid 436 through 453 Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.837A pdb=" N ILE B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 492 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 509 through 522 removed outlier: 3.756A pdb=" N GLU B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 543 Processing helix chain 'B' and resid 546 through 554 Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.814A pdb=" N LYS B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 25 through 42 removed outlier: 3.705A pdb=" N LYS C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 108 removed outlier: 3.596A pdb=" N THR C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.972A pdb=" N SER C 120 " --> pdb=" O ASN C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 140 through 152 removed outlier: 4.052A pdb=" N TYR C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.823A pdb=" N CYS C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 232 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 5.680A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) 542 hydrogen bonds defined for protein. 1617 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: 0.93 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2881 1.34 - 1.46: 1327 1.46 - 1.58: 4432 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 8694 Sorted by residual: bond pdb=" N TRP B 206 " pdb=" CA TRP B 206 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.32e-02 5.74e+03 1.07e+01 bond pdb=" N PHE B 188 " pdb=" CA PHE B 188 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.15e-02 7.56e+03 6.80e+00 bond pdb=" C ALA B 205 " pdb=" N TRP B 206 " ideal model delta sigma weight residual 1.331 1.360 -0.030 1.48e-02 4.57e+03 4.04e+00 bond pdb=" C TRP B 206 " pdb=" N THR B 207 " ideal model delta sigma weight residual 1.333 1.305 0.027 1.45e-02 4.76e+03 3.57e+00 bond pdb=" C TYR A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.28e-02 6.10e+03 2.82e+00 ... (remaining 8689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 11565 2.14 - 4.28: 264 4.28 - 6.42: 55 6.42 - 8.57: 10 8.57 - 10.71: 4 Bond angle restraints: 11898 Sorted by residual: angle pdb=" N VAL A 304 " pdb=" CA VAL A 304 " pdb=" C VAL A 304 " ideal model delta sigma weight residual 112.12 107.16 4.96 8.40e-01 1.42e+00 3.48e+01 angle pdb=" N VAL B 560 " pdb=" CA VAL B 560 " pdb=" C VAL B 560 " ideal model delta sigma weight residual 113.53 108.82 4.71 9.80e-01 1.04e+00 2.31e+01 angle pdb=" C HIS A 198 " pdb=" N LEU A 199 " pdb=" CA LEU A 199 " ideal model delta sigma weight residual 120.60 127.47 -6.87 1.60e+00 3.91e-01 1.84e+01 angle pdb=" C THR A 277 " pdb=" N ARG A 278 " pdb=" CA ARG A 278 " ideal model delta sigma weight residual 120.38 126.54 -6.16 1.46e+00 4.69e-01 1.78e+01 angle pdb=" N PHE B 188 " pdb=" CA PHE B 188 " pdb=" C PHE B 188 " ideal model delta sigma weight residual 112.03 106.86 5.17 1.31e+00 5.83e-01 1.56e+01 ... (remaining 11893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4486 17.58 - 35.17: 532 35.17 - 52.75: 142 52.75 - 70.33: 44 70.33 - 87.91: 13 Dihedral angle restraints: 5217 sinusoidal: 1722 harmonic: 3495 Sorted by residual: dihedral pdb=" CA TYR A 420 " pdb=" C TYR A 420 " pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA PHE A 249 " pdb=" C PHE A 249 " pdb=" N SER A 250 " pdb=" CA SER A 250 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLU A 295 " pdb=" C GLU A 295 " pdb=" N VAL A 296 " pdb=" CA VAL A 296 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 5214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1203 0.058 - 0.116: 207 0.116 - 0.174: 19 0.174 - 0.233: 4 0.233 - 0.291: 2 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CB ILE C 14 " pdb=" CA ILE C 14 " pdb=" CG1 ILE C 14 " pdb=" CG2 ILE C 14 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CG LEU A 327 " pdb=" CB LEU A 327 " pdb=" CD1 LEU A 327 " pdb=" CD2 LEU A 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE C 259 " pdb=" CA ILE C 259 " pdb=" CG1 ILE C 259 " pdb=" CG2 ILE C 259 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1432 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B 206 " 0.026 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C TRP B 206 " -0.092 2.00e-02 2.50e+03 pdb=" O TRP B 206 " 0.034 2.00e-02 2.50e+03 pdb=" N THR B 207 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 50 " -0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO A 51 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 205 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ALA B 205 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA B 205 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP B 206 " -0.014 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 158 2.67 - 3.23: 8939 3.23 - 3.79: 14036 3.79 - 4.34: 16844 4.34 - 4.90: 27040 Nonbonded interactions: 67017 Sorted by model distance: nonbonded pdb=" OG1 THR A 279 " pdb=" OE1 GLU A 280 " model vdw 2.114 3.040 nonbonded pdb=" O GLY C 169 " pdb=" OG SER C 201 " model vdw 2.177 3.040 nonbonded pdb=" O ALA B 335 " pdb=" OG1 THR B 341 " model vdw 2.195 3.040 nonbonded pdb=" O LEU A 359 " pdb=" N PHE A 363 " model vdw 2.202 3.120 nonbonded pdb=" O LYS C 36 " pdb=" OG1 THR C 40 " model vdw 2.218 3.040 ... (remaining 67012 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.890 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 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 : 0.003 0.062 8694 Z= 0.174 Angle : 0.806 10.707 11898 Z= 0.441 Chirality : 0.045 0.291 1435 Planarity : 0.005 0.086 1557 Dihedral : 18.000 87.915 2933 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.55 % Favored : 91.19 % Rotamer: Outliers : 7.03 % Allowed : 31.87 % Favored : 61.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.25), residues: 1175 helix: 0.36 (0.19), residues: 791 sheet: -5.71 (0.85), residues: 10 loop : -2.55 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 297 TYR 0.013 0.001 TYR B 391 PHE 0.016 0.002 PHE A 532 TRP 0.028 0.002 TRP C 13 HIS 0.006 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 8694) covalent geometry : angle 0.80621 / 0.44 (11898) hydrogen bonds : bond 0.13305 / 9.88 ( 542) hydrogen bonds : angle 5.97896 / 4.35 ( 1617) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 97 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.4178 (mttm) REVERT: A 206 MET cc_start: 0.6154 (mmt) cc_final: 0.5912 (mmp) REVERT: A 242 ILE cc_start: 0.5301 (OUTLIER) cc_final: 0.4958 (mp) REVERT: A 442 MET cc_start: 0.5639 (ppp) cc_final: 0.5364 (ppp) REVERT: A 474 GLN cc_start: 0.1582 (OUTLIER) cc_final: 0.0846 (pm20) REVERT: A 493 MET cc_start: 0.7159 (tmm) cc_final: 0.6201 (tmm) REVERT: B 332 LEU cc_start: 0.7861 (mm) cc_final: 0.7190 (mt) REVERT: B 512 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5442 (tp) REVERT: C 186 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.6930 (tt) REVERT: C 243 LEU cc_start: 0.2478 (OUTLIER) cc_final: 0.2014 (tt) outliers start: 56 outliers final: 43 residues processed: 146 average time/residue: 0.0623 time to fit residues: 14.0403 Evaluate side-chains 140 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 91 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS B 305 ASN ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN C 18 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.162166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.160701 restraints weight = 17732.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.160023 restraints weight = 23841.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.159315 restraints weight = 27343.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.158634 restraints weight = 25505.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.157947 restraints weight = 32797.164| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4373 r_free = 0.4373 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4373 r_free = 0.4373 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8694 Z= 0.187 Angle : 0.795 8.407 11898 Z= 0.412 Chirality : 0.047 0.214 1435 Planarity : 0.005 0.052 1557 Dihedral : 5.719 34.332 1248 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.55 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.02 (0.25), residues: 1175 helix: 0.25 (0.18), residues: 813 sheet: -5.78 (0.83), residues: 10 loop : -2.67 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 110 TYR 0.032 0.002 TYR A 285 PHE 0.022 0.003 PHE A 532 TRP 0.030 0.002 TRP B 206 HIS 0.012 0.002 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 ( 8694) covalent geometry : angle 0.79477 / 0.41 (11898) hydrogen bonds : bond 0.05197 / 3.81 ( 542) hydrogen bonds : angle 5.09379 / 3.68 ( 1617) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 VAL cc_start: 0.7320 (t) cc_final: 0.7116 (p) REVERT: B 258 GLU cc_start: 0.7843 (pp20) cc_final: 0.6890 (pt0) REVERT: B 305 ASN cc_start: 0.5463 (m-40) cc_final: 0.5259 (m110) REVERT: B 320 MET cc_start: 0.6821 (ppp) cc_final: 0.5980 (ppp) REVERT: B 332 LEU cc_start: 0.7636 (mm) cc_final: 0.7188 (mt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0573 time to fit residues: 12.4159 Evaluate side-chains 101 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 0.0020 chunk 47 optimal weight: 0.0370 chunk 75 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.5068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN C 18 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.164620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.164428 restraints weight = 17339.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 96)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.159525 restraints weight = 21571.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.159142 restraints weight = 29585.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.159167 restraints weight = 25994.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.159141 restraints weight = 23905.578| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4371 r_free = 0.4371 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4371 r_free = 0.4371 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8694 Z= 0.151 Angle : 0.724 10.267 11898 Z= 0.372 Chirality : 0.044 0.189 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.518 33.097 1248 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.55 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.87 (0.25), residues: 1175 helix: 0.34 (0.18), residues: 815 sheet: -5.87 (0.75), residues: 10 loop : -2.56 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.015 0.001 TYR A 153 PHE 0.019 0.002 PHE B 188 TRP 0.030 0.002 TRP C 13 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 8694) covalent geometry : angle 0.72383 / 0.37 (11898) hydrogen bonds : bond 0.04563 / 3.37 ( 542) hydrogen bonds : angle 4.83172 / 3.49 ( 1617) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 110 LEU cc_start: 0.4216 (tt) cc_final: 0.2537 (mt) REVERT: A 493 MET cc_start: 0.7178 (tmm) cc_final: 0.5895 (ttt) REVERT: B 258 GLU cc_start: 0.7515 (pp20) cc_final: 0.6930 (pt0) REVERT: B 305 ASN cc_start: 0.5148 (m-40) cc_final: 0.4916 (m110) REVERT: B 320 MET cc_start: 0.6702 (ppp) cc_final: 0.5951 (ppp) REVERT: B 332 LEU cc_start: 0.7338 (mm) cc_final: 0.6938 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0637 time to fit residues: 13.1237 Evaluate side-chains 104 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 0.5980 chunk 68 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 79 optimal weight: 0.0070 chunk 21 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 63 optimal weight: 0.0040 overall best weight: 0.5010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN C 191 HIS ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.164215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.163615 restraints weight = 17488.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.163472 restraints weight = 27891.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.163443 restraints weight = 26398.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 102)---------------| | r_work = 0.4353 r_free = 0.4353 target = 0.157844 restraints weight = 21081.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.157371 restraints weight = 25215.663| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4332 r_free = 0.4332 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4332 r_free = 0.4332 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8694 Z= 0.144 Angle : 0.692 8.601 11898 Z= 0.357 Chirality : 0.043 0.198 1435 Planarity : 0.005 0.058 1557 Dihedral : 5.388 31.012 1248 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.13 % Favored : 91.70 % Rotamer: Outliers : 0.13 % Allowed : 4.02 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.76 (0.25), residues: 1175 helix: 0.44 (0.18), residues: 822 sheet: -5.95 (0.72), residues: 10 loop : -2.61 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.018 0.002 TYR B 488 PHE 0.020 0.002 PHE A 532 TRP 0.030 0.001 TRP C 13 HIS 0.005 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8694) covalent geometry : angle 0.69242 / 0.36 (11898) hydrogen bonds : bond 0.04290 / 3.18 ( 542) hydrogen bonds : angle 4.66821 / 3.36 ( 1617) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 110 LEU cc_start: 0.3717 (tt) cc_final: 0.2306 (mt) REVERT: A 485 ASN cc_start: 0.4949 (t0) cc_final: 0.4437 (t0) REVERT: A 493 MET cc_start: 0.7128 (tmm) cc_final: 0.5944 (ttt) REVERT: A 506 MET cc_start: 0.7062 (tmm) cc_final: 0.6860 (tmm) REVERT: B 258 GLU cc_start: 0.7660 (pp20) cc_final: 0.7183 (pt0) REVERT: B 320 MET cc_start: 0.6656 (ppp) cc_final: 0.5924 (ppp) REVERT: B 332 LEU cc_start: 0.7391 (mm) cc_final: 0.6941 (mt) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.0665 time to fit residues: 13.8585 Evaluate side-chains 103 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 570 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.163007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.153160 restraints weight = 174956.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.155589 restraints weight = 109528.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.155309 restraints weight = 95414.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.154389 restraints weight = 95266.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.154361 restraints weight = 91085.604| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4214 r_free = 0.4214 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4214 r_free = 0.4214 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8694 Z= 0.152 Angle : 0.723 10.798 11898 Z= 0.369 Chirality : 0.044 0.183 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.351 31.168 1248 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.71 (0.25), residues: 1175 helix: 0.50 (0.19), residues: 817 sheet: -5.92 (0.75), residues: 10 loop : -2.61 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.017 0.001 TYR C 107 PHE 0.021 0.002 PHE B 188 TRP 0.030 0.001 TRP C 13 HIS 0.005 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8694) covalent geometry : angle 0.72339 / 0.37 (11898) hydrogen bonds : bond 0.04281 / 3.15 ( 542) hydrogen bonds : angle 4.65993 / 3.37 ( 1617) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.6852 (mmm) cc_final: 0.6113 (mmt) REVERT: A 485 ASN cc_start: 0.5693 (t0) cc_final: 0.5188 (t0) REVERT: A 493 MET cc_start: 0.7199 (tmm) cc_final: 0.5942 (ttt) REVERT: B 258 GLU cc_start: 0.7794 (pp20) cc_final: 0.7260 (pt0) REVERT: B 305 ASN cc_start: 0.5497 (m-40) cc_final: 0.5215 (m110) REVERT: B 320 MET cc_start: 0.6878 (ppp) cc_final: 0.6239 (ppp) REVERT: B 332 LEU cc_start: 0.7499 (mm) cc_final: 0.7111 (mt) REVERT: C 229 ASN cc_start: 0.7039 (m-40) cc_final: 0.6179 (p0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0634 time to fit residues: 12.4972 Evaluate side-chains 106 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** 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 = 0.4419 r_free = 0.4419 target = 0.162150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.152213 restraints weight = 177846.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.154269 restraints weight = 114427.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.153621 restraints weight = 95964.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.153504 restraints weight = 96920.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.153474 restraints weight = 89716.717| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4196 r_free = 0.4196 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4196 r_free = 0.4196 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8694 Z= 0.151 Angle : 0.715 9.991 11898 Z= 0.365 Chirality : 0.043 0.181 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.324 30.921 1248 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.81 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.71 (0.25), residues: 1175 helix: 0.49 (0.19), residues: 819 sheet: -5.91 (0.76), residues: 10 loop : -2.62 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 49 TYR 0.017 0.001 TYR A 285 PHE 0.034 0.002 PHE C 146 TRP 0.034 0.002 TRP C 13 HIS 0.005 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8694) covalent geometry : angle 0.71538 / 0.36 (11898) hydrogen bonds : bond 0.04278 / 3.14 ( 542) hydrogen bonds : angle 4.63465 / 3.36 ( 1617) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.6868 (mmm) cc_final: 0.6129 (mmt) REVERT: A 485 ASN cc_start: 0.5537 (t0) cc_final: 0.5043 (t0) REVERT: A 493 MET cc_start: 0.7138 (tmm) cc_final: 0.5881 (ttt) REVERT: B 258 GLU cc_start: 0.7836 (pp20) cc_final: 0.7268 (pt0) REVERT: B 263 GLN cc_start: 0.6780 (mm-40) cc_final: 0.6129 (tm-30) REVERT: B 305 ASN cc_start: 0.5525 (m-40) cc_final: 0.5262 (m110) REVERT: B 320 MET cc_start: 0.7020 (ppp) cc_final: 0.6450 (ppp) REVERT: B 332 LEU cc_start: 0.7518 (mm) cc_final: 0.7278 (mt) REVERT: C 229 ASN cc_start: 0.7142 (m-40) cc_final: 0.6307 (p0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0610 time to fit residues: 12.0507 Evaluate side-chains 99 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 3.9990 chunk 72 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.0000 chunk 6 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 overall best weight: 0.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 HIS ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN B 570 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.165110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.155810 restraints weight = 172216.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.158711 restraints weight = 106238.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.157319 restraints weight = 92370.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.157259 restraints weight = 90509.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.157152 restraints weight = 83290.135| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4246 r_free = 0.4246 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4246 r_free = 0.4246 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8694 Z= 0.135 Angle : 0.694 8.465 11898 Z= 0.350 Chirality : 0.042 0.197 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.126 29.692 1248 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.21 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -0.58 (0.25), residues: 1175 helix: 0.61 (0.19), residues: 818 sheet: -6.21 (0.59), residues: 10 loop : -2.60 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.013 0.001 TYR A 153 PHE 0.033 0.002 PHE C 146 TRP 0.039 0.001 TRP C 13 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8694) covalent geometry : angle 0.69369 / 0.35 (11898) hydrogen bonds : bond 0.03959 / 2.91 ( 542) hydrogen bonds : angle 4.59730 / 3.35 ( 1617) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6384 (tt0) REVERT: A 110 LEU cc_start: 0.4444 (tt) cc_final: 0.2817 (mt) REVERT: A 344 MET cc_start: 0.6995 (mmm) cc_final: 0.6210 (mmt) REVERT: A 393 LEU cc_start: 0.3031 (pt) cc_final: 0.2599 (mm) REVERT: A 493 MET cc_start: 0.6696 (tmm) cc_final: 0.5973 (ttt) REVERT: B 258 GLU cc_start: 0.7667 (pp20) cc_final: 0.7125 (pt0) REVERT: B 263 GLN cc_start: 0.6587 (mm-40) cc_final: 0.6178 (tm-30) REVERT: B 301 ILE cc_start: 0.6891 (tp) cc_final: 0.6577 (tp) REVERT: B 303 TYR cc_start: 0.4117 (t80) cc_final: 0.3568 (t80) REVERT: B 305 ASN cc_start: 0.5402 (m-40) cc_final: 0.5004 (m110) REVERT: B 320 MET cc_start: 0.6759 (ppp) cc_final: 0.6290 (ppp) REVERT: B 332 LEU cc_start: 0.7529 (mm) cc_final: 0.7281 (mt) REVERT: C 229 ASN cc_start: 0.6903 (m-40) cc_final: 0.6163 (p0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0604 time to fit residues: 11.7732 Evaluate side-chains 103 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.160588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4401 r_free = 0.4401 target = 0.160100 restraints weight = 17872.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.152736 restraints weight = 27546.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.152457 restraints weight = 32180.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.152463 restraints weight = 29202.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.152494 restraints weight = 24929.738| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4258 r_free = 0.4258 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4258 r_free = 0.4258 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8694 Z= 0.160 Angle : 0.741 13.180 11898 Z= 0.373 Chirality : 0.044 0.201 1435 Planarity : 0.005 0.051 1557 Dihedral : 5.271 30.417 1248 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.98 % Favored : 90.85 % Rotamer: Outliers : 0.13 % Allowed : 1.38 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.25), residues: 1175 helix: 0.54 (0.19), residues: 820 sheet: -6.26 (0.55), residues: 10 loop : -2.65 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 89 TYR 0.028 0.002 TYR A 285 PHE 0.029 0.002 PHE C 146 TRP 0.037 0.002 TRP C 13 HIS 0.005 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 8694) covalent geometry : angle 0.74060 / 0.37 (11898) hydrogen bonds : bond 0.04238 / 3.10 ( 542) hydrogen bonds : angle 4.64866 / 3.37 ( 1617) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.7220 (mmm) cc_final: 0.6605 (mmt) REVERT: A 393 LEU cc_start: 0.3109 (pt) cc_final: 0.2557 (mm) REVERT: A 493 MET cc_start: 0.6797 (tmm) cc_final: 0.6086 (ttp) REVERT: B 320 MET cc_start: 0.6778 (ppp) cc_final: 0.6273 (ppp) REVERT: B 332 LEU cc_start: 0.7516 (mm) cc_final: 0.7219 (mt) REVERT: C 252 HIS cc_start: 0.4879 (OUTLIER) cc_final: 0.4073 (m90) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.0539 time to fit residues: 10.3377 Evaluate side-chains 102 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 48 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** C 241 HIS ** 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 = 0.4432 r_free = 0.4432 target = 0.163244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.153576 restraints weight = 174386.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.155440 restraints weight = 109716.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.154975 restraints weight = 91369.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.154834 restraints weight = 99837.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.154908 restraints weight = 91344.637| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8694 Z= 0.141 Angle : 0.713 11.131 11898 Z= 0.359 Chirality : 0.043 0.191 1435 Planarity : 0.005 0.054 1557 Dihedral : 5.132 28.705 1248 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.38 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1175 helix: 0.64 (0.19), residues: 816 sheet: -6.37 (0.50), residues: 10 loop : -2.59 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 110 TYR 0.016 0.001 TYR A 285 PHE 0.028 0.002 PHE C 146 TRP 0.040 0.001 TRP C 13 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 8694) covalent geometry : angle 0.71276 / 0.36 (11898) hydrogen bonds : bond 0.03985 / 2.92 ( 542) hydrogen bonds : angle 4.59666 / 3.34 ( 1617) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 LEU cc_start: 0.3327 (pt) cc_final: 0.2839 (mm) REVERT: A 493 MET cc_start: 0.6729 (tmm) cc_final: 0.5922 (ttp) REVERT: A 501 LEU cc_start: 0.6166 (mp) cc_final: 0.5935 (mp) REVERT: B 258 GLU cc_start: 0.7743 (pp20) cc_final: 0.7174 (pt0) REVERT: B 263 GLN cc_start: 0.5703 (mm-40) cc_final: 0.5254 (tm-30) REVERT: B 320 MET cc_start: 0.6956 (ppp) cc_final: 0.6553 (ppp) REVERT: B 332 LEU cc_start: 0.7468 (mm) cc_final: 0.7206 (mt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0648 time to fit residues: 11.9408 Evaluate side-chains 99 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 0.0010 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS C 229 ASN ** C 241 HIS ** 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 = 0.4417 r_free = 0.4417 target = 0.161877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.151737 restraints weight = 178450.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.154603 restraints weight = 111743.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.152864 restraints weight = 93030.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.152863 restraints weight = 96712.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.152923 restraints weight = 86979.792| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4188 r_free = 0.4188 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4188 r_free = 0.4188 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8694 Z= 0.149 Angle : 0.729 13.276 11898 Z= 0.366 Chirality : 0.043 0.194 1435 Planarity : 0.005 0.052 1557 Dihedral : 5.178 30.112 1248 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.64 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1175 helix: 0.61 (0.19), residues: 818 sheet: -6.43 (0.50), residues: 10 loop : -2.52 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.017 0.001 TYR A 285 PHE 0.027 0.002 PHE C 146 TRP 0.038 0.001 TRP C 13 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8694) covalent geometry : angle 0.72860 / 0.37 (11898) hydrogen bonds : bond 0.04105 / 3.00 ( 542) hydrogen bonds : angle 4.59730 / 3.33 ( 1617) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LEU cc_start: 0.5215 (mm) cc_final: 0.4977 (mm) REVERT: A 393 LEU cc_start: 0.3510 (pt) cc_final: 0.2941 (mm) REVERT: A 419 GLU cc_start: 0.6251 (pt0) cc_final: 0.6031 (pt0) REVERT: A 485 ASN cc_start: 0.5190 (t0) cc_final: 0.4788 (t0) REVERT: A 493 MET cc_start: 0.6927 (tmm) cc_final: 0.6024 (ttp) REVERT: B 263 GLN cc_start: 0.5762 (mm-40) cc_final: 0.5220 (tm-30) REVERT: B 303 TYR cc_start: 0.4336 (t80) cc_final: 0.3575 (t80) REVERT: B 320 MET cc_start: 0.7066 (ppp) cc_final: 0.6591 (ppp) REVERT: B 332 LEU cc_start: 0.7499 (mm) cc_final: 0.7246 (mt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0634 time to fit residues: 12.0367 Evaluate side-chains 101 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 51 optimal weight: 0.0050 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.162232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.152434 restraints weight = 178422.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.155109 restraints weight = 111602.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.154259 restraints weight = 99339.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.153702 restraints weight = 97768.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.153643 restraints weight = 95244.882| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8694 Z= 0.144 Angle : 0.718 12.356 11898 Z= 0.360 Chirality : 0.043 0.189 1435 Planarity : 0.005 0.054 1557 Dihedral : 5.110 28.568 1248 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.64 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -0.52 (0.25), residues: 1175 helix: 0.65 (0.19), residues: 818 sheet: -6.48 (0.46), residues: 10 loop : -2.56 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.015 0.001 TYR A 153 PHE 0.027 0.002 PHE C 146 TRP 0.039 0.001 TRP C 13 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8694) covalent geometry : angle 0.71839 / 0.36 (11898) hydrogen bonds : bond 0.04002 / 2.94 ( 542) hydrogen bonds : angle 4.59340 / 3.34 ( 1617) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1322.14 seconds wall clock time: 23 minutes 33.63 seconds (1413.63 seconds total)