Starting phenix.real_space_refine on Tue Feb 3 19:32:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vx4_32168/02_2026/7vx4_32168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx4_32168/02_2026/7vx4_32168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vx4_32168/02_2026/7vx4_32168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx4_32168/02_2026/7vx4_32168.map" model { file = "/net/cci-nas-00/data/ceres_data/7vx4_32168/02_2026/7vx4_32168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx4_32168/02_2026/7vx4_32168.cif" } resolution = 3.9 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= -0.002 sd= 0.062 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 Zn 1 6.06 5 S 37 5.16 5 C 4152 2.51 5 N 1070 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6493 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1545 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1576 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.46, per 1000 atoms: 0.38 Number of scatterers: 6493 At special positions: 0 Unit cell: (77.603, 101.649, 118.044, 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) Zn 1 29.99 S 37 16.00 O 1233 8.00 N 1070 7.00 C 4152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 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 Links applied NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 53 " " NAG E1301 " - " ASN E 343 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 423.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 58.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.660A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.954A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.742A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.511A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.826A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.560A pdb=" N LYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.615A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.750A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.677A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.598A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.599A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.780A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.824A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.098A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.579A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 414 removed outlier: 4.396A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.599A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.407A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.750A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.990A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.773A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.729A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.648A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.948A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.585A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.102A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.140A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.923A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 273 hydrogen bonds defined for protein. 769 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2081 1.34 - 1.46: 1727 1.46 - 1.58: 2810 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6676 Sorted by residual: bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.38e+00 ... (remaining 6671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8930 1.97 - 3.95: 135 3.95 - 5.92: 12 5.92 - 7.90: 0 7.90 - 9.87: 1 Bond angle restraints: 9078 Sorted by residual: angle pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta sigma weight residual 121.98 131.85 -9.87 3.11e+00 1.03e-01 1.01e+01 angle pdb=" N TYR E 505 " pdb=" CA TYR E 505 " pdb=" C TYR E 505 " ideal model delta sigma weight residual 111.36 114.77 -3.41 1.09e+00 8.42e-01 9.78e+00 angle pdb=" N ASP A 136 " pdb=" CA ASP A 136 " pdb=" C ASP A 136 " ideal model delta sigma weight residual 111.07 114.15 -3.08 1.07e+00 8.73e-01 8.31e+00 angle pdb=" N VAL A 293 " pdb=" CA VAL A 293 " pdb=" C VAL A 293 " ideal model delta sigma weight residual 112.83 110.26 2.57 9.90e-01 1.02e+00 6.75e+00 angle pdb=" C LYS A 363 " pdb=" N VAL A 364 " pdb=" CA VAL A 364 " ideal model delta sigma weight residual 122.43 119.17 3.26 1.26e+00 6.30e-01 6.71e+00 ... (remaining 9073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 3883 16.02 - 32.05: 77 32.05 - 48.07: 33 48.07 - 64.09: 8 64.09 - 80.12: 3 Dihedral angle restraints: 4004 sinusoidal: 1675 harmonic: 2329 Sorted by residual: dihedral pdb=" CA PHE E 497 " pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N GLY A 147 " pdb=" CA GLY A 147 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA E 352 " pdb=" C ALA E 352 " pdb=" N TRP E 353 " pdb=" CA TRP E 353 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 584 0.030 - 0.061: 242 0.061 - 0.091: 91 0.091 - 0.121: 42 0.121 - 0.151: 4 Chirality restraints: 963 Sorted by residual: chirality pdb=" C1 NAG E1301 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E1301 " pdb=" O5 NAG E1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA TYR E 505 " pdb=" N TYR E 505 " pdb=" C TYR E 505 " pdb=" CB TYR E 505 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 960 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 504 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C GLY E 504 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY E 504 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR E 505 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 611 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 612 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 612 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 612 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.012 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR E 495 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.001 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 87 2.65 - 3.21: 6043 3.21 - 3.77: 9658 3.77 - 4.34: 13646 4.34 - 4.90: 22092 Nonbonded interactions: 51526 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.082 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.189 2.230 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.225 3.040 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.234 3.040 ... (remaining 51521 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 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 0.135 6690 Z= 0.165 Angle : 0.629 9.874 9107 Z= 0.393 Chirality : 0.042 0.151 963 Planarity : 0.004 0.038 1172 Dihedral : 8.878 80.115 2491 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 0.89 % Favored : 98.98 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.27 (0.26), residues: 789 helix: -2.59 (0.20), residues: 372 sheet: -0.28 (0.66), residues: 50 loop : -0.21 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.025 0.001 TYR E 495 PHE 0.020 0.002 PHE E 497 TRP 0.014 0.001 TRP A 302 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6676) covalent geometry : angle 0.62704 ( 9078) SS BOND : bond 0.00151 ( 7) SS BOND : angle 0.95740 ( 14) hydrogen bonds : bond 0.28753 ( 273) hydrogen bonds : angle 9.28745 ( 769) metal coordination : bond 0.11493 ( 2) link_NAG-ASN : bond 0.00157 ( 5) link_NAG-ASN : angle 1.14301 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.8877 (m) cc_final: 0.8445 (p) REVERT: A 102 GLN cc_start: 0.7965 (pt0) cc_final: 0.7399 (pp30) REVERT: A 198 ASP cc_start: 0.8375 (p0) cc_final: 0.8070 (p0) REVERT: A 243 TYR cc_start: 0.8400 (t80) cc_final: 0.8044 (t80) REVERT: A 295 ASP cc_start: 0.7665 (m-30) cc_final: 0.7325 (t70) REVERT: A 442 GLN cc_start: 0.8439 (mm110) cc_final: 0.8126 (mt0) REVERT: A 484 ILE cc_start: 0.8329 (mt) cc_final: 0.8082 (mt) REVERT: A 559 ARG cc_start: 0.8692 (ptm-80) cc_final: 0.8192 (ttp-110) REVERT: A 584 LEU cc_start: 0.7155 (tp) cc_final: 0.6869 (tt) REVERT: E 334 ASN cc_start: 0.7192 (t0) cc_final: 0.6826 (m-40) REVERT: E 335 LEU cc_start: 0.7554 (mt) cc_final: 0.7285 (mt) REVERT: E 356 LYS cc_start: 0.8642 (tttp) cc_final: 0.8399 (ttpp) REVERT: E 422 ASN cc_start: 0.7524 (m-40) cc_final: 0.7094 (m110) REVERT: E 519 HIS cc_start: 0.6695 (m-70) cc_final: 0.6467 (t-170) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0926 time to fit residues: 27.8310 Evaluate side-chains 126 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 61 ASN A 524 GLN A 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.207138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.172571 restraints weight = 17648.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.179316 restraints weight = 16438.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.182471 restraints weight = 7502.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.183003 restraints weight = 5399.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.184297 restraints weight = 4713.798| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6690 Z= 0.150 Angle : 0.648 9.433 9107 Z= 0.337 Chirality : 0.045 0.161 963 Planarity : 0.005 0.032 1172 Dihedral : 5.595 43.556 969 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.16 % Allowed : 10.92 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.28), residues: 789 helix: -0.63 (0.24), residues: 381 sheet: -0.10 (0.65), residues: 44 loop : 0.14 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 582 TYR 0.024 0.002 TYR E 495 PHE 0.025 0.002 PHE A 308 TRP 0.027 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6676) covalent geometry : angle 0.64179 ( 9078) SS BOND : bond 0.00285 ( 7) SS BOND : angle 1.34492 ( 14) hydrogen bonds : bond 0.05259 ( 273) hydrogen bonds : angle 5.48956 ( 769) metal coordination : bond 0.00356 ( 2) link_NAG-ASN : bond 0.00173 ( 5) link_NAG-ASN : angle 1.90602 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7988 (mttt) cc_final: 0.7756 (mtpt) REVERT: A 222 LEU cc_start: 0.8113 (tp) cc_final: 0.7645 (tp) REVERT: A 249 MET cc_start: 0.6234 (tmm) cc_final: 0.5866 (tmm) REVERT: A 295 ASP cc_start: 0.7658 (m-30) cc_final: 0.7232 (t70) REVERT: A 299 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7446 (t0) outliers start: 20 outliers final: 12 residues processed: 148 average time/residue: 0.0625 time to fit residues: 12.8029 Evaluate side-chains 115 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 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 24 GLN A 101 GLN A 373 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN A 599 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.173434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.142856 restraints weight = 18373.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.148444 restraints weight = 24447.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.150577 restraints weight = 8102.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.153361 restraints weight = 5717.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.153569 restraints weight = 4607.344| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6690 Z= 0.164 Angle : 0.630 8.363 9107 Z= 0.327 Chirality : 0.045 0.183 963 Planarity : 0.004 0.036 1172 Dihedral : 5.140 33.130 969 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.30 % Allowed : 11.78 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.18 (0.29), residues: 789 helix: -0.18 (0.25), residues: 397 sheet: -0.13 (0.66), residues: 45 loop : 0.20 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 582 TYR 0.021 0.002 TYR E 495 PHE 0.026 0.002 PHE E 497 TRP 0.027 0.002 TRP A 594 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6676) covalent geometry : angle 0.62613 ( 9078) SS BOND : bond 0.00319 ( 7) SS BOND : angle 1.26504 ( 14) hydrogen bonds : bond 0.04586 ( 273) hydrogen bonds : angle 5.22721 ( 769) metal coordination : bond 0.00047 ( 2) link_NAG-ASN : bond 0.00107 ( 5) link_NAG-ASN : angle 1.39067 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.254 Fit side-chains REVERT: A 26 LYS cc_start: 0.8198 (mttt) cc_final: 0.7907 (mtpt) REVERT: A 222 LEU cc_start: 0.8012 (tp) cc_final: 0.7736 (tp) REVERT: A 295 ASP cc_start: 0.7919 (m-30) cc_final: 0.7344 (t0) REVERT: A 323 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7437 (mmm) outliers start: 21 outliers final: 14 residues processed: 126 average time/residue: 0.0701 time to fit residues: 12.2996 Evaluate side-chains 106 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 8 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.0270 chunk 75 optimal weight: 0.8980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 417 HIS A 598 GLN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.172260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.141116 restraints weight = 17199.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.146711 restraints weight = 21127.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.148365 restraints weight = 8019.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.150097 restraints weight = 5935.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.151093 restraints weight = 5675.541| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6690 Z= 0.124 Angle : 0.595 7.878 9107 Z= 0.302 Chirality : 0.043 0.180 963 Planarity : 0.004 0.036 1172 Dihedral : 4.775 31.503 969 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.73 % Allowed : 13.51 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.01 (0.29), residues: 789 helix: 0.11 (0.26), residues: 395 sheet: -0.21 (0.68), residues: 49 loop : 0.13 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 582 TYR 0.017 0.001 TYR E 495 PHE 0.019 0.002 PHE E 497 TRP 0.022 0.002 TRP A 594 HIS 0.002 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6676) covalent geometry : angle 0.58950 ( 9078) SS BOND : bond 0.00209 ( 7) SS BOND : angle 0.96911 ( 14) hydrogen bonds : bond 0.04046 ( 273) hydrogen bonds : angle 5.08108 ( 769) metal coordination : bond 0.00020 ( 2) link_NAG-ASN : bond 0.00077 ( 5) link_NAG-ASN : angle 1.86899 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8084 (mttt) cc_final: 0.7865 (mtpt) REVERT: A 222 LEU cc_start: 0.8036 (tp) cc_final: 0.7750 (tp) REVERT: A 291 ILE cc_start: 0.6185 (OUTLIER) cc_final: 0.5583 (tp) REVERT: A 295 ASP cc_start: 0.7673 (m-30) cc_final: 0.7229 (t0) REVERT: A 305 GLN cc_start: 0.7730 (tp40) cc_final: 0.7356 (tp40) outliers start: 17 outliers final: 12 residues processed: 114 average time/residue: 0.0513 time to fit residues: 8.5190 Evaluate side-chains 105 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 20.0000 chunk 41 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 598 GLN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.165844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.136333 restraints weight = 12402.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.139190 restraints weight = 13880.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.140548 restraints weight = 9589.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.142862 restraints weight = 6395.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.143563 restraints weight = 5612.212| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6690 Z= 0.143 Angle : 0.589 8.320 9107 Z= 0.302 Chirality : 0.044 0.213 963 Planarity : 0.004 0.036 1172 Dihedral : 4.671 30.705 969 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.59 % Allowed : 12.79 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.09 (0.29), residues: 789 helix: 0.23 (0.26), residues: 396 sheet: -0.26 (0.68), residues: 49 loop : 0.11 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 273 TYR 0.017 0.002 TYR E 495 PHE 0.018 0.002 PHE E 497 TRP 0.025 0.002 TRP A 594 HIS 0.002 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6676) covalent geometry : angle 0.58539 ( 9078) SS BOND : bond 0.00273 ( 7) SS BOND : angle 0.91828 ( 14) hydrogen bonds : bond 0.03992 ( 273) hydrogen bonds : angle 5.07000 ( 769) metal coordination : bond 0.00116 ( 2) link_NAG-ASN : bond 0.00043 ( 5) link_NAG-ASN : angle 1.49120 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8208 (mttt) cc_final: 0.7963 (mtpt) REVERT: A 100 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7844 (tt) REVERT: A 222 LEU cc_start: 0.8032 (tp) cc_final: 0.7773 (tp) REVERT: A 291 ILE cc_start: 0.6143 (OUTLIER) cc_final: 0.5500 (tp) REVERT: A 295 ASP cc_start: 0.7757 (m-30) cc_final: 0.7431 (t0) REVERT: A 598 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7182 (mp-120) outliers start: 23 outliers final: 17 residues processed: 107 average time/residue: 0.0556 time to fit residues: 8.6186 Evaluate side-chains 106 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 598 GLN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.162950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.132487 restraints weight = 18079.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.138486 restraints weight = 21696.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.140900 restraints weight = 7151.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141753 restraints weight = 5116.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.142685 restraints weight = 4692.370| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6690 Z= 0.169 Angle : 0.604 8.880 9107 Z= 0.310 Chirality : 0.045 0.204 963 Planarity : 0.004 0.037 1172 Dihedral : 4.687 30.572 969 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.59 % Allowed : 13.65 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.08 (0.29), residues: 789 helix: 0.27 (0.26), residues: 402 sheet: -0.34 (0.69), residues: 49 loop : 0.05 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.017 0.002 TYR E 495 PHE 0.019 0.002 PHE E 497 TRP 0.019 0.002 TRP A 594 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6676) covalent geometry : angle 0.60062 ( 9078) SS BOND : bond 0.00347 ( 7) SS BOND : angle 1.00653 ( 14) hydrogen bonds : bond 0.04044 ( 273) hydrogen bonds : angle 5.11500 ( 769) metal coordination : bond 0.00020 ( 2) link_NAG-ASN : bond 0.00073 ( 5) link_NAG-ASN : angle 1.49151 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.246 Fit side-chains REVERT: A 26 LYS cc_start: 0.8162 (mttt) cc_final: 0.7952 (mtpt) REVERT: A 62 MET cc_start: 0.8611 (tmm) cc_final: 0.8357 (tpp) REVERT: A 100 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7927 (tt) REVERT: A 222 LEU cc_start: 0.8111 (tp) cc_final: 0.7894 (tt) REVERT: A 291 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5708 (tp) REVERT: A 295 ASP cc_start: 0.7960 (m-30) cc_final: 0.7661 (t0) REVERT: A 482 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7599 (mtp85) outliers start: 23 outliers final: 18 residues processed: 108 average time/residue: 0.0601 time to fit residues: 9.0575 Evaluate side-chains 109 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.165324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.133822 restraints weight = 12982.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.136624 restraints weight = 15039.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.138111 restraints weight = 9205.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141364 restraints weight = 6017.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.141890 restraints weight = 4615.459| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6690 Z= 0.125 Angle : 0.569 9.239 9107 Z= 0.291 Chirality : 0.043 0.202 963 Planarity : 0.004 0.037 1172 Dihedral : 4.500 30.203 969 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.45 % Allowed : 14.94 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.22 (0.29), residues: 789 helix: 0.44 (0.27), residues: 401 sheet: -0.32 (0.72), residues: 47 loop : 0.06 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.015 0.001 TYR E 508 PHE 0.014 0.002 PHE A 308 TRP 0.015 0.001 TRP A 478 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6676) covalent geometry : angle 0.56420 ( 9078) SS BOND : bond 0.00208 ( 7) SS BOND : angle 0.88046 ( 14) hydrogen bonds : bond 0.03818 ( 273) hydrogen bonds : angle 5.05683 ( 769) metal coordination : bond 0.00009 ( 2) link_NAG-ASN : bond 0.00124 ( 5) link_NAG-ASN : angle 1.84406 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8137 (mttt) cc_final: 0.7922 (mtpt) REVERT: A 62 MET cc_start: 0.8701 (tmm) cc_final: 0.8469 (tpp) REVERT: A 100 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8011 (tt) REVERT: A 222 LEU cc_start: 0.8031 (tp) cc_final: 0.7809 (tt) REVERT: A 295 ASP cc_start: 0.8003 (m-30) cc_final: 0.7617 (t0) REVERT: A 482 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7590 (mtp85) outliers start: 22 outliers final: 17 residues processed: 112 average time/residue: 0.0667 time to fit residues: 10.1143 Evaluate side-chains 110 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.164748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.133558 restraints weight = 14509.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.138989 restraints weight = 16118.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.140222 restraints weight = 7251.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.140822 restraints weight = 5342.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.141881 restraints weight = 5291.406| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6690 Z= 0.119 Angle : 0.620 13.080 9107 Z= 0.306 Chirality : 0.044 0.253 963 Planarity : 0.004 0.037 1172 Dihedral : 5.579 58.687 969 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.45 % Allowed : 15.66 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.29 (0.30), residues: 789 helix: 0.54 (0.27), residues: 403 sheet: -0.27 (0.73), residues: 47 loop : 0.03 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.012 0.001 TYR E 508 PHE 0.014 0.001 PHE A 308 TRP 0.021 0.001 TRP A 302 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6676) covalent geometry : angle 0.58701 ( 9078) SS BOND : bond 0.00195 ( 7) SS BOND : angle 0.85081 ( 14) hydrogen bonds : bond 0.03656 ( 273) hydrogen bonds : angle 4.92909 ( 769) metal coordination : bond 0.00012 ( 2) link_NAG-ASN : bond 0.00582 ( 5) link_NAG-ASN : angle 4.88846 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.238 Fit side-chains REVERT: A 222 LEU cc_start: 0.8085 (tp) cc_final: 0.7856 (tt) REVERT: A 295 ASP cc_start: 0.7793 (m-30) cc_final: 0.7472 (t0) REVERT: A 353 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8326 (ttpt) REVERT: A 475 LYS cc_start: 0.8392 (tttt) cc_final: 0.8181 (tmtt) REVERT: A 482 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7545 (mtp85) outliers start: 22 outliers final: 18 residues processed: 112 average time/residue: 0.0657 time to fit residues: 10.1290 Evaluate side-chains 111 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.164293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.135799 restraints weight = 13342.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.139223 restraints weight = 17781.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.140560 restraints weight = 10208.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.141512 restraints weight = 6846.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.142242 restraints weight = 6708.082| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6690 Z= 0.136 Angle : 0.622 13.882 9107 Z= 0.308 Chirality : 0.045 0.284 963 Planarity : 0.004 0.039 1172 Dihedral : 4.842 49.220 969 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.87 % Allowed : 16.81 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.29 (0.30), residues: 789 helix: 0.59 (0.27), residues: 400 sheet: -0.34 (0.73), residues: 47 loop : -0.04 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.013 0.001 TYR E 453 PHE 0.015 0.002 PHE E 429 TRP 0.027 0.002 TRP A 302 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6676) covalent geometry : angle 0.59195 ( 9078) SS BOND : bond 0.00234 ( 7) SS BOND : angle 0.89207 ( 14) hydrogen bonds : bond 0.03755 ( 273) hydrogen bonds : angle 4.96209 ( 769) metal coordination : bond 0.00020 ( 2) link_NAG-ASN : bond 0.00577 ( 5) link_NAG-ASN : angle 4.67839 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8850 (tpp) cc_final: 0.8599 (tpp) REVERT: A 295 ASP cc_start: 0.7741 (m-30) cc_final: 0.7506 (t0) REVERT: A 482 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7589 (mtp85) REVERT: A 598 GLN cc_start: 0.7709 (tp40) cc_final: 0.7094 (tm-30) outliers start: 18 outliers final: 18 residues processed: 112 average time/residue: 0.0565 time to fit residues: 8.9189 Evaluate side-chains 110 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 30 optimal weight: 7.9990 chunk 62 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.0060 chunk 53 optimal weight: 0.9980 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.166652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.141590 restraints weight = 19305.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.145558 restraints weight = 25390.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.147130 restraints weight = 8162.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.150522 restraints weight = 5798.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.150205 restraints weight = 3945.303| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6690 Z= 0.116 Angle : 0.617 13.386 9107 Z= 0.305 Chirality : 0.043 0.262 963 Planarity : 0.004 0.037 1172 Dihedral : 4.640 43.415 969 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.87 % Allowed : 17.10 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.35 (0.30), residues: 789 helix: 0.63 (0.27), residues: 400 sheet: -0.25 (0.73), residues: 47 loop : -0.00 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.013 0.001 TYR A 385 PHE 0.015 0.001 PHE A 308 TRP 0.028 0.001 TRP A 302 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6676) covalent geometry : angle 0.58771 ( 9078) SS BOND : bond 0.00179 ( 7) SS BOND : angle 0.84012 ( 14) hydrogen bonds : bond 0.03598 ( 273) hydrogen bonds : angle 4.89478 ( 769) metal coordination : bond 0.00008 ( 2) link_NAG-ASN : bond 0.00422 ( 5) link_NAG-ASN : angle 4.58984 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8833 (tpp) cc_final: 0.8573 (tpp) REVERT: A 482 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7524 (mtp85) REVERT: A 598 GLN cc_start: 0.7564 (tp40) cc_final: 0.7080 (tm-30) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.0520 time to fit residues: 8.1328 Evaluate side-chains 109 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain E residue 334 ASN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 33 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.168450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.145717 restraints weight = 22765.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.148454 restraints weight = 26984.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.150788 restraints weight = 8620.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.153251 restraints weight = 5291.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.153142 restraints weight = 3573.500| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6690 Z= 0.119 Angle : 0.608 12.872 9107 Z= 0.300 Chirality : 0.043 0.229 963 Planarity : 0.004 0.037 1172 Dihedral : 4.632 42.902 969 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.73 % Allowed : 17.10 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.40 (0.30), residues: 789 helix: 0.69 (0.27), residues: 400 sheet: -0.25 (0.73), residues: 47 loop : -0.01 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.012 0.001 TYR A 385 PHE 0.014 0.001 PHE A 308 TRP 0.030 0.002 TRP A 302 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6676) covalent geometry : angle 0.58160 ( 9078) SS BOND : bond 0.00185 ( 7) SS BOND : angle 0.81629 ( 14) hydrogen bonds : bond 0.03495 ( 273) hydrogen bonds : angle 4.85175 ( 769) metal coordination : bond 0.00003 ( 2) link_NAG-ASN : bond 0.00487 ( 5) link_NAG-ASN : angle 4.34406 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1137.40 seconds wall clock time: 20 minutes 15.29 seconds (1215.29 seconds total)