Starting phenix.real_space_refine on Sun Apr 5 06:37:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5r_61150/04_2026/9j5r_61150.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5r_61150/04_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_61150/04_2026/9j5r_61150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5r_61150/04_2026/9j5r_61150.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5r_61150/04_2026/9j5r_61150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5r_61150/04_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-2.1rc1-6017/lib/python3.9/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2.43, per 1000 atoms: 0.28 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: 0.62 Conformation dependent library (CDL) restraints added in 368.6 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: 0.19 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: 1.05 Time building geometry restraints manager: 0.76 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.830 Find NCS groups from input model: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 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 covalent geometry : bond 0.00348 ( 8694) covalent geometry : angle 0.80621 (11898) hydrogen bonds : bond 0.13305 ( 542) hydrogen bonds : angle 5.97896 ( 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 : 0.233 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: 0.0619 time to fit residues: 13.8939 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 : 0.207 ------------------------------------------------------------------------------- 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: 0.1980 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: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 264 GLN ** 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 167 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.162924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.161051 restraints weight = 17695.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.160928 restraints weight = 22386.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.160798 restraints weight = 20941.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.160465 restraints weight = 23911.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.160464 restraints weight = 19938.462| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4407 r_free = 0.4407 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4407 r_free = 0.4407 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8694 Z= 0.179 Angle : 0.783 8.204 11898 Z= 0.405 Chirality : 0.047 0.221 1435 Planarity : 0.005 0.051 1557 Dihedral : 5.686 33.759 1248 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.38 % Favored : 91.53 % Rotamer: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % 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: -1.00 (0.25), residues: 1175 helix: 0.26 (0.18), residues: 814 sheet: -5.78 (0.84), residues: 10 loop : -2.64 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 110 TYR 0.031 0.002 TYR A 285 PHE 0.021 0.003 PHE A 532 TRP 0.030 0.002 TRP B 206 HIS 0.006 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8694) covalent geometry : angle 0.78345 (11898) hydrogen bonds : bond 0.05118 ( 542) hydrogen bonds : angle 5.07675 ( 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 141 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.6653 (mmt) cc_final: 0.6295 (mmt) REVERT: A 559 VAL cc_start: 0.7312 (t) cc_final: 0.7103 (p) REVERT: B 204 SER cc_start: 0.8332 (m) cc_final: 0.8036 (p) REVERT: B 258 GLU cc_start: 0.7817 (pp20) cc_final: 0.6848 (pt0) REVERT: B 320 MET cc_start: 0.6835 (ppp) cc_final: 0.6063 (ppp) REVERT: B 332 LEU cc_start: 0.7639 (mm) cc_final: 0.7174 (mt) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.0580 time to fit residues: 12.9735 Evaluate side-chains 105 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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: 4.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 0.0070 chunk 75 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 305 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 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 = 0.4457 r_free = 0.4457 target = 0.165005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.163667 restraints weight = 17618.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.162818 restraints weight = 21354.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.162214 restraints weight = 29061.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.162235 restraints weight = 23194.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.162241 restraints weight = 21346.428| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4424 r_free = 0.4424 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4424 r_free = 0.4424 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.2388 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= 0.150 Angle : 0.717 10.416 11898 Z= 0.369 Chirality : 0.044 0.194 1435 Planarity : 0.005 0.059 1557 Dihedral : 5.467 32.466 1248 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.64 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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: -0.88 (0.25), residues: 1175 helix: 0.36 (0.18), residues: 817 sheet: -5.77 (0.81), residues: 10 loop : -2.65 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 505 TYR 0.016 0.002 TYR A 153 PHE 0.019 0.002 PHE A 532 TRP 0.031 0.002 TRP C 13 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8694) covalent geometry : angle 0.71681 (11898) hydrogen bonds : bond 0.04496 ( 542) hydrogen bonds : angle 4.82496 ( 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 : 0.290 Fit side-chains revert: symmetry clash REVERT: A 110 LEU cc_start: 0.4114 (tt) cc_final: 0.2383 (mt) REVERT: A 493 MET cc_start: 0.7131 (tmm) cc_final: 0.5850 (ttt) REVERT: A 559 VAL cc_start: 0.7260 (t) cc_final: 0.7051 (p) REVERT: B 204 SER cc_start: 0.8362 (m) cc_final: 0.7988 (p) REVERT: B 258 GLU cc_start: 0.7494 (pp20) cc_final: 0.6915 (pt0) REVERT: B 305 ASN cc_start: 0.5131 (m-40) cc_final: 0.4901 (m110) REVERT: B 320 MET cc_start: 0.6742 (ppp) cc_final: 0.5988 (ppp) REVERT: B 332 LEU cc_start: 0.7293 (mm) cc_final: 0.6901 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0622 time to fit residues: 12.8787 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 : 0.299 ------------------------------------------------------------------------------- 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: 0.4980 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 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 = 0.4426 r_free = 0.4426 target = 0.162561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.162521 restraints weight = 17801.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.162520 restraints weight = 21628.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.162510 restraints weight = 23143.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.162504 restraints weight = 25995.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.162506 restraints weight = 18745.553| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4425 r_free = 0.4425 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4425 r_free = 0.4425 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8694 Z= 0.152 Angle : 0.705 9.007 11898 Z= 0.364 Chirality : 0.044 0.205 1435 Planarity : 0.005 0.058 1557 Dihedral : 5.414 31.799 1248 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.73 % Favored : 91.19 % Rotamer: Outliers : 0.25 % Allowed : 3.89 % 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: -0.79 (0.25), residues: 1175 helix: 0.40 (0.18), residues: 824 sheet: -5.81 (0.80), residues: 10 loop : -2.61 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 49 TYR 0.017 0.002 TYR A 285 PHE 0.019 0.002 PHE A 532 TRP 0.031 0.002 TRP C 13 HIS 0.005 0.001 HIS C 59 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8694) covalent geometry : angle 0.70516 (11898) hydrogen bonds : bond 0.04357 ( 542) hydrogen bonds : angle 4.71054 ( 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: 2 poor density : 135 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.3947 (tt) cc_final: 0.2307 (mt) REVERT: A 485 ASN cc_start: 0.5042 (t0) cc_final: 0.4513 (t0) REVERT: A 506 MET cc_start: 0.7135 (tmm) cc_final: 0.6926 (tmm) REVERT: A 559 VAL cc_start: 0.7211 (t) cc_final: 0.6991 (p) REVERT: B 204 SER cc_start: 0.8106 (m) cc_final: 0.7788 (p) REVERT: B 258 GLU cc_start: 0.7666 (pp20) cc_final: 0.7215 (pt0) REVERT: B 305 ASN cc_start: 0.5179 (m-40) cc_final: 0.4978 (m110) REVERT: B 320 MET cc_start: 0.6663 (ppp) cc_final: 0.5944 (ppp) REVERT: B 332 LEU cc_start: 0.7280 (mm) cc_final: 0.6886 (mt) outliers start: 2 outliers final: 1 residues processed: 137 average time/residue: 0.0607 time to fit residues: 12.8026 Evaluate side-chains 107 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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: 0.8980 chunk 88 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.0270 chunk 91 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.162612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.160064 restraints weight = 17800.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.159674 restraints weight = 29802.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.159546 restraints weight = 26138.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.159410 restraints weight = 22905.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.159490 restraints weight = 18210.941| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4390 r_free = 0.4390 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4390 r_free = 0.4390 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5409 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8694 Z= 0.150 Angle : 0.721 10.828 11898 Z= 0.368 Chirality : 0.044 0.196 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.359 30.755 1248 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.55 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: -0.74 (0.25), residues: 1175 helix: 0.44 (0.18), residues: 823 sheet: -5.87 (0.78), residues: 10 loop : -2.59 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.019 0.001 TYR B 488 PHE 0.020 0.002 PHE A 532 TRP 0.034 0.002 TRP C 13 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8694) covalent geometry : angle 0.72139 (11898) hydrogen bonds : bond 0.04295 ( 542) hydrogen bonds : angle 4.70417 ( 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 127 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 110 LEU cc_start: 0.3874 (tt) cc_final: 0.2399 (mt) REVERT: A 344 MET cc_start: 0.6744 (mmm) cc_final: 0.6208 (mmt) REVERT: A 485 ASN cc_start: 0.4908 (t0) cc_final: 0.4401 (t0) REVERT: B 204 SER cc_start: 0.8199 (m) cc_final: 0.7866 (p) REVERT: B 258 GLU cc_start: 0.7688 (pp20) cc_final: 0.7123 (pt0) REVERT: B 305 ASN cc_start: 0.5166 (m-40) cc_final: 0.4921 (m110) REVERT: B 320 MET cc_start: 0.6625 (ppp) cc_final: 0.5961 (ppp) REVERT: B 332 LEU cc_start: 0.7335 (mm) cc_final: 0.6942 (mt) REVERT: C 229 ASN cc_start: 0.6635 (m-40) cc_final: 0.5960 (p0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0663 time to fit residues: 13.0036 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 80 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4388 r_free = 0.4388 target = 0.159159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.156279 restraints weight = 17850.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.152907 restraints weight = 25782.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.151330 restraints weight = 21524.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.151117 restraints weight = 26423.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.151381 restraints weight = 20861.885| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8694 Z= 0.173 Angle : 0.745 9.549 11898 Z= 0.382 Chirality : 0.045 0.198 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.483 32.519 1248 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.15 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -0.85 (0.25), residues: 1175 helix: 0.35 (0.18), residues: 823 sheet: -5.99 (0.75), residues: 10 loop : -2.61 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 49 TYR 0.020 0.002 TYR A 285 PHE 0.033 0.002 PHE C 146 TRP 0.033 0.002 TRP C 13 HIS 0.006 0.001 HIS C 59 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8694) covalent geometry : angle 0.74456 (11898) hydrogen bonds : bond 0.04615 ( 542) hydrogen bonds : angle 4.76083 ( 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 120 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.7150 (mmm) cc_final: 0.6315 (mmt) REVERT: A 485 ASN cc_start: 0.4846 (t0) cc_final: 0.4353 (t0) REVERT: A 506 MET cc_start: 0.7221 (tmm) cc_final: 0.7014 (tmm) REVERT: B 204 SER cc_start: 0.8325 (m) cc_final: 0.7971 (p) REVERT: B 305 ASN cc_start: 0.5231 (m-40) cc_final: 0.4909 (m110) REVERT: B 320 MET cc_start: 0.6838 (ppp) cc_final: 0.6126 (ppp) REVERT: B 332 LEU cc_start: 0.7642 (mm) cc_final: 0.7386 (mt) REVERT: C 229 ASN cc_start: 0.6941 (m-40) cc_final: 0.6175 (p0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0698 time to fit residues: 12.6160 Evaluate side-chains 95 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.2980 chunk 12 optimal weight: 0.0000 chunk 76 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 85 optimal weight: 0.0370 chunk 48 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 167 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 = 0.4430 r_free = 0.4430 target = 0.163136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.153693 restraints weight = 174158.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.156046 restraints weight = 111826.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.155857 restraints weight = 94876.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.154824 restraints weight = 94528.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.154923 restraints weight = 92204.594| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 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 = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.3169 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= 0.143 Angle : 0.705 8.782 11898 Z= 0.358 Chirality : 0.043 0.183 1435 Planarity : 0.005 0.057 1557 Dihedral : 5.224 30.836 1248 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.47 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -0.67 (0.25), residues: 1175 helix: 0.53 (0.19), residues: 818 sheet: -6.15 (0.62), residues: 10 loop : -2.61 (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 285 PHE 0.030 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 covalent geometry : bond 0.00308 ( 8694) covalent geometry : angle 0.70522 (11898) hydrogen bonds : bond 0.04127 ( 542) hydrogen bonds : angle 4.68037 ( 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 118 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.6979 (mmm) cc_final: 0.6216 (mmt) REVERT: A 393 LEU cc_start: 0.3173 (pt) cc_final: 0.2572 (mm) REVERT: A 493 MET cc_start: 0.6666 (tmm) cc_final: 0.5992 (ttp) REVERT: A 506 MET cc_start: 0.7109 (tmm) cc_final: 0.6547 (tmm) REVERT: B 204 SER cc_start: 0.8441 (m) cc_final: 0.8010 (p) REVERT: B 258 GLU cc_start: 0.7801 (pp20) cc_final: 0.7258 (pt0) REVERT: B 263 GLN cc_start: 0.5895 (mm-40) cc_final: 0.5129 (tm-30) REVERT: B 320 MET cc_start: 0.6846 (ppp) cc_final: 0.6307 (ppp) REVERT: B 332 LEU cc_start: 0.7577 (mm) cc_final: 0.7287 (mt) REVERT: C 229 ASN cc_start: 0.6798 (m-40) cc_final: 0.6109 (p0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0678 time to fit residues: 12.2169 Evaluate side-chains 97 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4420 r_free = 0.4420 target = 0.162055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.152202 restraints weight = 178599.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.154595 restraints weight = 113224.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.153535 restraints weight = 95065.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.153364 restraints weight = 98645.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.153315 restraints weight = 89997.971| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4193 r_free = 0.4193 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4193 r_free = 0.4193 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5688 moved from start: 0.3326 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= 0.148 Angle : 0.726 13.064 11898 Z= 0.365 Chirality : 0.043 0.188 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.233 30.007 1248 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.55 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % 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: -0.68 (0.25), residues: 1175 helix: 0.51 (0.19), residues: 820 sheet: -6.30 (0.54), residues: 10 loop : -2.59 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.026 0.002 TYR A 285 PHE 0.029 0.002 PHE C 146 TRP 0.038 0.002 TRP C 13 HIS 0.005 0.001 HIS C 59 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8694) covalent geometry : angle 0.72609 (11898) hydrogen bonds : bond 0.04152 ( 542) hydrogen bonds : angle 4.68138 ( 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 115 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 LEU cc_start: 0.3390 (pt) cc_final: 0.2896 (mm) REVERT: A 493 MET cc_start: 0.6789 (tmm) cc_final: 0.6093 (ttp) REVERT: A 501 LEU cc_start: 0.6041 (mp) cc_final: 0.5835 (mp) REVERT: B 204 SER cc_start: 0.8460 (m) cc_final: 0.8014 (p) REVERT: B 263 GLN cc_start: 0.5896 (mm-40) cc_final: 0.5246 (tm-30) REVERT: B 298 MET cc_start: 0.5378 (tpt) cc_final: 0.4560 (mtp) REVERT: B 320 MET cc_start: 0.7086 (ppp) cc_final: 0.6573 (ppp) REVERT: B 332 LEU cc_start: 0.7548 (mm) cc_final: 0.7161 (mt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0622 time to fit residues: 11.3833 Evaluate side-chains 97 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 97 optimal weight: 0.0070 chunk 6 optimal weight: 0.0000 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN B 305 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.163517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.153934 restraints weight = 175884.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.157074 restraints weight = 107434.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.155300 restraints weight = 92182.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.155539 restraints weight = 96097.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.155188 restraints weight = 90445.833| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4222 r_free = 0.4222 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4222 r_free = 0.4222 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8694 Z= 0.141 Angle : 0.710 11.208 11898 Z= 0.358 Chirality : 0.043 0.181 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.172 28.402 1248 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.47 % Favored : 91.27 % 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: -0.64 (0.25), residues: 1175 helix: 0.55 (0.19), residues: 821 sheet: -6.40 (0.50), residues: 10 loop : -2.60 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 89 TYR 0.016 0.001 TYR A 153 PHE 0.027 0.002 PHE C 146 TRP 0.040 0.001 TRP C 13 HIS 0.006 0.001 HIS C 59 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8694) covalent geometry : angle 0.70965 (11898) hydrogen bonds : bond 0.04048 ( 542) hydrogen bonds : angle 4.62893 ( 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 121 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 LEU cc_start: 0.3143 (pt) cc_final: 0.2783 (mm) REVERT: A 493 MET cc_start: 0.6805 (tmm) cc_final: 0.6098 (ttp) REVERT: A 501 LEU cc_start: 0.6031 (mp) cc_final: 0.5805 (mp) REVERT: B 204 SER cc_start: 0.8374 (m) cc_final: 0.7964 (p) REVERT: B 258 GLU cc_start: 0.7784 (pp20) cc_final: 0.7181 (pt0) REVERT: B 263 GLN cc_start: 0.5705 (mm-40) cc_final: 0.4985 (tm-30) REVERT: B 298 MET cc_start: 0.5135 (tpt) cc_final: 0.4356 (mtp) REVERT: B 303 TYR cc_start: 0.4255 (t80) cc_final: 0.3503 (t80) REVERT: B 320 MET cc_start: 0.6945 (ppp) cc_final: 0.6429 (ppp) REVERT: B 332 LEU cc_start: 0.7555 (mm) cc_final: 0.7199 (mt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0693 time to fit residues: 12.7012 Evaluate side-chains 98 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 113 optimal weight: 0.0070 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 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 = 0.4438 r_free = 0.4438 target = 0.163634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.153909 restraints weight = 174097.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.155999 restraints weight = 110316.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.155141 restraints weight = 94327.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.155142 restraints weight = 98703.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.155254 restraints weight = 89735.630| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4233 r_free = 0.4233 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4233 r_free = 0.4233 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5613 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8694 Z= 0.139 Angle : 0.711 12.917 11898 Z= 0.356 Chirality : 0.042 0.182 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.098 28.615 1248 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.47 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.62 (0.19), residues: 821 sheet: -6.47 (0.48), residues: 10 loop : -2.60 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.016 0.001 TYR A 153 PHE 0.026 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 covalent geometry : bond 0.00298 ( 8694) covalent geometry : angle 0.71138 (11898) hydrogen bonds : bond 0.03934 ( 542) hydrogen bonds : angle 4.56730 ( 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 119 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 LEU cc_start: 0.3498 (pt) cc_final: 0.3005 (mm) REVERT: A 485 ASN cc_start: 0.4906 (t0) cc_final: 0.4501 (t0) REVERT: A 493 MET cc_start: 0.6682 (tmm) cc_final: 0.5946 (ttp) REVERT: A 501 LEU cc_start: 0.6041 (mp) cc_final: 0.5788 (mp) REVERT: B 258 GLU cc_start: 0.7785 (pp20) cc_final: 0.7164 (pt0) REVERT: B 263 GLN cc_start: 0.5782 (mm-40) cc_final: 0.5068 (tm-30) REVERT: B 298 MET cc_start: 0.5190 (tpt) cc_final: 0.4533 (mtp) REVERT: B 303 TYR cc_start: 0.4145 (t80) cc_final: 0.3421 (t80) REVERT: B 320 MET cc_start: 0.6919 (ppp) cc_final: 0.6474 (ppp) REVERT: B 332 LEU cc_start: 0.7466 (mm) cc_final: 0.7052 (mt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0613 time to fit residues: 11.2440 Evaluate side-chains 102 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4419 r_free = 0.4419 target = 0.161717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.160151 restraints weight = 17961.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.154749 restraints weight = 24422.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.153934 restraints weight = 30502.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.153800 restraints weight = 32970.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.154024 restraints weight = 24835.270| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5567 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= 0.146 Angle : 0.722 12.368 11898 Z= 0.362 Chirality : 0.043 0.186 1435 Planarity : 0.005 0.056 1557 Dihedral : 5.126 27.752 1248 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.81 % Favored : 91.02 % Rotamer: Outliers : 0.13 % Allowed : 0.50 % 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: -0.56 (0.25), residues: 1175 helix: 0.66 (0.19), residues: 818 sheet: -6.56 (0.43), residues: 10 loop : -2.68 (0.32), residues: 347 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 0.025 0.002 PHE C 146 TRP 0.037 0.001 TRP C 13 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8694) covalent geometry : angle 0.72180 (11898) hydrogen bonds : bond 0.04060 ( 542) hydrogen bonds : angle 4.56521 ( 1617) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1262.22 seconds wall clock time: 22 minutes 35.52 seconds (1355.52 seconds total)