Starting phenix.real_space_refine on Fri Sep 11 01:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vx4_32168/09_2026/7vx4_32168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx4_32168/09_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_32168/09_2026/7vx4_32168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx4_32168/09_2026/7vx4_32168.map" model { file = "/net/cci-nas-00/data/ceres_data/7vx4_32168/09_2026/7vx4_32168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx4_32168/09_2026/7vx4_32168.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vx4_32168/09_2026/7vx4_32168.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vx4_32168/09_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-2.2.1-6174/lib/python3.11/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 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 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: 0.43 Conformation dependent library (CDL) restraints added in 618.8 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: 0.21 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: 1.00 Time building geometry restraints manager: 0.64 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: 3794 16.02 - 32.05: 71 32.05 - 48.07: 25 48.07 - 64.09: 6 64.09 - 80.12: 3 Dihedral angle restraints: 3899 sinusoidal: 1570 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 3896 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 : 8.486 80.115 2386 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/Z covalent geometry : bond 0.00280 / 0.15 ( 6676) covalent geometry : angle 0.62704 / 0.39 ( 9078) SS BOND : bond 0.00151 / 0.08 ( 7) SS BOND : angle 0.95740 / 0.58 ( 14) hydrogen bonds : bond 0.28753 / 18.87 ( 273) hydrogen bonds : angle 9.28745 / 6.48 ( 769) metal coordination : bond 0.11493 / 5.66 ( 2) link_NAG-ASN : bond 0.00157 / 0.08 ( 5) link_NAG-ASN : angle 1.14301 / 0.65 ( 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 : 0.254 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: 0.0929 time to fit residues: 28.2453 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 : 0.242 ------------------------------------------------------------------------------- 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... 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 = 0.4221 r_free = 0.4221 target = 0.206755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.172105 restraints weight = 17565.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.179180 restraints weight = 16354.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.182218 restraints weight = 7255.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.182784 restraints weight = 5263.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.184042 restraints weight = 4561.767| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 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 = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6690 Z= 0.148 Angle : 0.650 9.651 9107 Z= 0.337 Chirality : 0.045 0.159 963 Planarity : 0.005 0.033 1172 Dihedral : 4.423 18.281 864 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.37 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: -0.54 (0.28), residues: 789 helix: -0.61 (0.24), residues: 381 sheet: -0.08 (0.65), residues: 44 loop : 0.14 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 582 TYR 0.024 0.002 TYR E 495 PHE 0.025 0.002 PHE A 308 TRP 0.028 0.002 TRP A 594 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6676) covalent geometry : angle 0.64539 / 0.34 ( 9078) SS BOND : bond 0.00284 / 0.15 ( 7) SS BOND : angle 1.27916 / 0.68 ( 14) hydrogen bonds : bond 0.04960 / 3.18 ( 273) hydrogen bonds : angle 5.44699 / 3.63 ( 769) metal coordination : bond 0.00295 / 0.15 ( 2) link_NAG-ASN : bond 0.00194 / 0.11 ( 5) link_NAG-ASN : angle 1.72431 / 0.97 ( 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 154 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7929 (mttt) cc_final: 0.7698 (mtpt) REVERT: A 222 LEU cc_start: 0.8097 (tp) cc_final: 0.7641 (tp) REVERT: A 249 MET cc_start: 0.6211 (tmm) cc_final: 0.5887 (tmm) REVERT: A 295 ASP cc_start: 0.7659 (m-30) cc_final: 0.7263 (t70) REVERT: A 299 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7532 (t0) outliers start: 20 outliers final: 12 residues processed: 149 average time/residue: 0.0756 time to fit residues: 15.5619 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 : 0.251 ------------------------------------------------------------------------------- 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: 0.5980 chunk 29 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.0030 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 101 GLN 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 = 0.4162 r_free = 0.4162 target = 0.200452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.164965 restraints weight = 19090.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.171626 restraints weight = 16348.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.173964 restraints weight = 7709.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.174947 restraints weight = 5363.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.176857 restraints weight = 4558.173| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4163 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= 0.151 Angle : 0.613 8.673 9107 Z= 0.317 Chirality : 0.045 0.200 963 Planarity : 0.004 0.035 1172 Dihedral : 4.362 19.629 864 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 3.02 % Allowed : 12.07 % 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: -0.11 (0.28), residues: 789 helix: -0.10 (0.25), residues: 391 sheet: -0.10 (0.66), residues: 45 loop : 0.21 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 514 TYR 0.020 0.002 TYR E 495 PHE 0.024 0.002 PHE E 497 TRP 0.026 0.002 TRP A 594 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 6676) covalent geometry : angle 0.60956 / 0.32 ( 9078) SS BOND : bond 0.00281 / 0.15 ( 7) SS BOND : angle 1.20532 / 0.65 ( 14) hydrogen bonds : bond 0.04527 / 2.95 ( 273) hydrogen bonds : angle 5.18817 / 3.43 ( 769) metal coordination : bond 0.00022 / 0.01 ( 2) link_NAG-ASN : bond 0.00074 / 0.04 ( 5) link_NAG-ASN : angle 1.24771 / 0.71 ( 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 134 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.302 Fit side-chains REVERT: A 26 LYS cc_start: 0.8295 (mttt) cc_final: 0.7974 (mtpt) REVERT: A 190 MET cc_start: 0.6479 (ttt) cc_final: 0.6272 (ttt) REVERT: A 222 LEU cc_start: 0.8013 (tp) cc_final: 0.7666 (tp) REVERT: A 295 ASP cc_start: 0.7947 (m-30) cc_final: 0.7297 (t0) REVERT: A 323 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7392 (mmm) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.0712 time to fit residues: 12.6959 Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 0.0050 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 HIS A 598 GLN A 599 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.166088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135325 restraints weight = 15799.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.142145 restraints weight = 19369.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.143104 restraints weight = 6736.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.143993 restraints weight = 5291.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.144975 restraints weight = 4945.657| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6690 Z= 0.159 Angle : 0.608 8.980 9107 Z= 0.313 Chirality : 0.045 0.187 963 Planarity : 0.004 0.048 1172 Dihedral : 4.430 18.646 864 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.16 % Allowed : 12.93 % Favored : 83.91 % 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: -0.06 (0.29), residues: 789 helix: 0.09 (0.26), residues: 395 sheet: -0.17 (0.67), residues: 49 loop : 0.04 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 273 TYR 0.019 0.002 TYR E 508 PHE 0.021 0.002 PHE E 497 TRP 0.019 0.002 TRP A 594 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 6676) covalent geometry : angle 0.60429 / 0.31 ( 9078) SS BOND : bond 0.00280 / 0.15 ( 7) SS BOND : angle 1.08505 / 0.58 ( 14) hydrogen bonds : bond 0.04269 / 2.78 ( 273) hydrogen bonds : angle 5.16014 / 3.42 ( 769) metal coordination : bond 0.00013 / 0.01 ( 2) link_NAG-ASN : bond 0.00085 / 0.05 ( 5) link_NAG-ASN : angle 1.64228 / 0.94 ( 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 116 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8175 (mttt) cc_final: 0.7868 (mtpt) REVERT: A 190 MET cc_start: 0.6679 (ttt) cc_final: 0.6429 (ttt) REVERT: A 222 LEU cc_start: 0.8069 (tp) cc_final: 0.7786 (tp) REVERT: A 291 ILE cc_start: 0.6285 (OUTLIER) cc_final: 0.5623 (tp) REVERT: A 295 ASP cc_start: 0.7888 (m-30) cc_final: 0.7477 (t0) outliers start: 20 outliers final: 16 residues processed: 111 average time/residue: 0.0646 time to fit residues: 10.5352 Evaluate side-chains 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 494 SER 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: 0.9980 chunk 11 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.165671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135912 restraints weight = 12389.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.139240 restraints weight = 15402.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.141026 restraints weight = 9324.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.141482 restraints weight = 6626.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.142236 restraints weight = 6278.752| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6690 Z= 0.139 Angle : 0.581 8.851 9107 Z= 0.298 Chirality : 0.044 0.197 963 Planarity : 0.004 0.036 1172 Dihedral : 4.299 18.861 864 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.88 % Allowed : 12.79 % Favored : 83.33 % 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: 0.14 (0.29), residues: 789 helix: 0.31 (0.26), residues: 395 sheet: -0.33 (0.67), residues: 49 loop : 0.10 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 355 TYR 0.016 0.001 TYR E 495 PHE 0.018 0.002 PHE E 497 TRP 0.021 0.001 TRP A 302 HIS 0.002 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6676) covalent geometry : angle 0.57805 / 0.30 ( 9078) SS BOND : bond 0.00235 / 0.13 ( 7) SS BOND : angle 0.96067 / 0.52 ( 14) hydrogen bonds : bond 0.03962 / 2.58 ( 273) hydrogen bonds : angle 5.02529 / 3.35 ( 769) metal coordination : bond 0.00023 / 0.01 ( 2) link_NAG-ASN : bond 0.00065 / 0.04 ( 5) link_NAG-ASN : angle 1.30057 / 0.75 ( 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 120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8235 (mttt) cc_final: 0.7954 (mtpt) REVERT: A 62 MET cc_start: 0.8732 (tmm) cc_final: 0.8409 (tpp) REVERT: A 190 MET cc_start: 0.6742 (ttt) cc_final: 0.6465 (ttt) REVERT: A 222 LEU cc_start: 0.8015 (tp) cc_final: 0.7772 (tp) REVERT: A 291 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5589 (tp) REVERT: A 295 ASP cc_start: 0.7694 (m-30) cc_final: 0.7419 (t0) REVERT: A 305 GLN cc_start: 0.7937 (tp40) cc_final: 0.7428 (tp40) REVERT: A 482 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7568 (mtp85) REVERT: A 598 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7632 (tp40) outliers start: 25 outliers final: 15 residues processed: 112 average time/residue: 0.0773 time to fit residues: 11.9375 Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.162434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.136036 restraints weight = 18149.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140786 restraints weight = 24729.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.142530 restraints weight = 8172.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.144273 restraints weight = 6114.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.144361 restraints weight = 5313.469| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6690 Z= 0.173 Angle : 0.594 7.335 9107 Z= 0.309 Chirality : 0.046 0.221 963 Planarity : 0.004 0.039 1172 Dihedral : 4.477 19.672 864 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.02 % Allowed : 14.08 % Favored : 81.90 % 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: 0.07 (0.29), residues: 789 helix: 0.35 (0.26), residues: 395 sheet: -0.49 (0.68), residues: 49 loop : -0.05 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 582 TYR 0.019 0.002 TYR E 495 PHE 0.020 0.002 PHE E 497 TRP 0.023 0.002 TRP A 302 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 6676) covalent geometry : angle 0.59087 / 0.31 ( 9078) SS BOND : bond 0.00347 / 0.19 ( 7) SS BOND : angle 1.03386 / 0.55 ( 14) hydrogen bonds : bond 0.04093 / 2.68 ( 273) hydrogen bonds : angle 5.11415 / 3.44 ( 769) metal coordination : bond 0.00079 / 0.04 ( 2) link_NAG-ASN : bond 0.00084 / 0.04 ( 5) link_NAG-ASN : angle 1.41651 / 0.83 ( 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 126 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8148 (mttt) cc_final: 0.7827 (mtpt) REVERT: A 190 MET cc_start: 0.6709 (ttt) cc_final: 0.6487 (ttt) REVERT: A 291 ILE cc_start: 0.6465 (OUTLIER) cc_final: 0.5829 (tp) REVERT: A 295 ASP cc_start: 0.7972 (m-30) cc_final: 0.7728 (t0) REVERT: A 305 GLN cc_start: 0.8003 (tp40) cc_final: 0.7545 (tp40) REVERT: E 347 PHE cc_start: 0.8583 (m-80) cc_final: 0.8230 (m-80) outliers start: 26 outliers final: 19 residues processed: 118 average time/residue: 0.0814 time to fit residues: 13.0937 Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 291 ILE 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 391 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 463 VAL 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 401 VAL 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: 0.6980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.162962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.135253 restraints weight = 13232.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138700 restraints weight = 17887.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.140691 restraints weight = 10283.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.140984 restraints weight = 7248.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.143063 restraints weight = 6564.332| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6690 Z= 0.145 Angle : 0.586 9.115 9107 Z= 0.300 Chirality : 0.044 0.222 963 Planarity : 0.004 0.036 1172 Dihedral : 4.350 18.493 864 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: 0.16 (0.29), residues: 789 helix: 0.45 (0.26), residues: 399 sheet: -0.42 (0.70), residues: 47 loop : -0.05 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.015 0.002 TYR E 495 PHE 0.016 0.002 PHE E 497 TRP 0.023 0.001 TRP A 302 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6676) covalent geometry : angle 0.58310 / 0.30 ( 9078) SS BOND : bond 0.00233 / 0.13 ( 7) SS BOND : angle 0.97513 / 0.52 ( 14) hydrogen bonds : bond 0.03956 / 2.54 ( 273) hydrogen bonds : angle 5.00566 / 3.35 ( 769) metal coordination : bond 0.00010 / 0.00 ( 2) link_NAG-ASN : bond 0.00081 / 0.04 ( 5) link_NAG-ASN : angle 1.30168 / 0.75 ( 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 116 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8188 (mttt) cc_final: 0.7913 (mtpt) REVERT: A 100 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7976 (tt) REVERT: A 190 MET cc_start: 0.6706 (ttt) cc_final: 0.6461 (ttt) REVERT: A 291 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.5839 (tp) REVERT: E 347 PHE cc_start: 0.8557 (m-80) cc_final: 0.8242 (m-80) outliers start: 22 outliers final: 17 residues processed: 110 average time/residue: 0.0676 time to fit residues: 10.6481 Evaluate side-chains 111 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 THR Chi-restraints excluded: chain A residue 291 ILE 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 391 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 444 LEU 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 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: 0.8980 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 HIS A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.161549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.131870 restraints weight = 14733.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.136772 restraints weight = 19261.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.138131 restraints weight = 8473.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.138830 restraints weight = 6073.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.139538 restraints weight = 6306.915| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6690 Z= 0.151 Angle : 0.613 10.077 9107 Z= 0.307 Chirality : 0.045 0.205 963 Planarity : 0.004 0.037 1172 Dihedral : 4.372 19.707 864 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.16 % Allowed : 16.09 % Favored : 80.75 % 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: 0.19 (0.30), residues: 789 helix: 0.54 (0.27), residues: 402 sheet: -0.49 (0.71), residues: 47 loop : -0.12 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.014 0.002 TYR E 453 PHE 0.018 0.002 PHE A 308 TRP 0.027 0.002 TRP A 302 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6676) covalent geometry : angle 0.60984 / 0.31 ( 9078) SS BOND : bond 0.00286 / 0.16 ( 7) SS BOND : angle 0.99698 / 0.53 ( 14) hydrogen bonds : bond 0.03837 / 2.48 ( 273) hydrogen bonds : angle 4.99618 / 3.35 ( 769) metal coordination : bond 0.00017 / 0.01 ( 2) link_NAG-ASN : bond 0.00075 / 0.04 ( 5) link_NAG-ASN : angle 1.33472 / 0.78 ( 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 118 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8099 (mttt) cc_final: 0.7852 (mtpt) REVERT: A 62 MET cc_start: 0.8803 (tpp) cc_final: 0.8599 (tpp) REVERT: A 190 MET cc_start: 0.6793 (ttt) cc_final: 0.6539 (ttt) REVERT: A 291 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.5887 (tp) REVERT: A 556 ASN cc_start: 0.8496 (m-40) cc_final: 0.8031 (m110) REVERT: A 598 GLN cc_start: 0.7637 (tp40) cc_final: 0.6774 (tm-30) REVERT: E 347 PHE cc_start: 0.8606 (m-80) cc_final: 0.8317 (m-80) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.0722 time to fit residues: 11.5648 Evaluate side-chains 112 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 291 ILE 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 444 LEU 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 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: 0.1980 chunk 55 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 11 optimal weight: 0.0000 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.165440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135550 restraints weight = 13247.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.140278 restraints weight = 17669.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.141739 restraints weight = 8161.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.142418 restraints weight = 5918.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.143046 restraints weight = 6211.256| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5811 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= 0.113 Angle : 0.576 9.371 9107 Z= 0.288 Chirality : 0.043 0.193 963 Planarity : 0.004 0.035 1172 Dihedral : 4.143 19.774 864 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.01 % Allowed : 17.53 % Favored : 80.46 % 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: 0.32 (0.30), residues: 789 helix: 0.64 (0.27), residues: 398 sheet: -0.43 (0.72), residues: 47 loop : -0.04 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 355 TYR 0.013 0.001 TYR A 207 PHE 0.016 0.001 PHE A 308 TRP 0.020 0.001 TRP A 302 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 6676) covalent geometry : angle 0.57431 / 0.29 ( 9078) SS BOND : bond 0.00138 / 0.08 ( 7) SS BOND : angle 0.87745 / 0.47 ( 14) hydrogen bonds : bond 0.03564 / 2.33 ( 273) hydrogen bonds : angle 4.88920 / 3.29 ( 769) metal coordination : bond 0.00011 / 0.01 ( 2) link_NAG-ASN : bond 0.00088 / 0.05 ( 5) link_NAG-ASN : angle 1.14362 / 0.66 ( 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 115 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.264 Fit side-chains REVERT: A 26 LYS cc_start: 0.8293 (mttt) cc_final: 0.8008 (mtpt) REVERT: A 190 MET cc_start: 0.6799 (ttt) cc_final: 0.6511 (ttt) REVERT: A 222 LEU cc_start: 0.7907 (tp) cc_final: 0.7600 (tp) REVERT: A 297 MET cc_start: 0.8937 (mmm) cc_final: 0.8329 (mmt) REVERT: A 437 ASN cc_start: 0.8697 (m-40) cc_final: 0.8419 (m110) REVERT: A 598 GLN cc_start: 0.7709 (tp40) cc_final: 0.6989 (tm-30) REVERT: E 347 PHE cc_start: 0.8434 (m-80) cc_final: 0.8181 (m-80) REVERT: E 420 ASP cc_start: 0.8389 (m-30) cc_final: 0.7977 (m-30) outliers start: 12 outliers final: 11 residues processed: 110 average time/residue: 0.0699 time to fit residues: 10.9818 Evaluate side-chains 105 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 444 LEU 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 385 THR Chi-restraints excluded: chain E residue 387 LEU 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: 0.5980 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 0.0010 chunk 26 optimal weight: 0.0670 chunk 24 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.167864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.139519 restraints weight = 19126.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.144801 restraints weight = 24292.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.146954 restraints weight = 7575.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.150496 restraints weight = 5292.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.150512 restraints weight = 3885.603| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6690 Z= 0.111 Angle : 0.586 9.170 9107 Z= 0.292 Chirality : 0.043 0.197 963 Planarity : 0.004 0.035 1172 Dihedral : 4.097 19.188 864 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.16 % Allowed : 18.10 % Favored : 79.74 % 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: 0.42 (0.30), residues: 789 helix: 0.68 (0.27), residues: 397 sheet: -0.24 (0.74), residues: 47 loop : 0.05 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 355 TYR 0.013 0.001 TYR A 183 PHE 0.016 0.001 PHE A 308 TRP 0.023 0.001 TRP A 302 HIS 0.002 0.000 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6676) covalent geometry : angle 0.58207 / 0.29 ( 9078) SS BOND : bond 0.00135 / 0.07 ( 7) SS BOND : angle 0.85403 / 0.46 ( 14) hydrogen bonds : bond 0.03572 / 2.29 ( 273) hydrogen bonds : angle 4.81028 / 3.23 ( 769) metal coordination : bond 0.00014 / 0.01 ( 2) link_NAG-ASN : bond 0.00205 / 0.10 ( 5) link_NAG-ASN : angle 1.57455 / 0.90 ( 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 116 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.248 Fit side-chains REVERT: A 62 MET cc_start: 0.8603 (tpp) cc_final: 0.8361 (tpt) REVERT: A 222 LEU cc_start: 0.7952 (tp) cc_final: 0.7652 (tp) REVERT: A 297 MET cc_start: 0.8750 (mmm) cc_final: 0.8185 (mmt) REVERT: A 299 ASP cc_start: 0.7743 (t0) cc_final: 0.7486 (t0) REVERT: A 380 GLN cc_start: 0.7991 (mt0) cc_final: 0.7785 (mt0) REVERT: A 437 ASN cc_start: 0.8600 (m-40) cc_final: 0.8348 (m110) REVERT: A 598 GLN cc_start: 0.7581 (tp40) cc_final: 0.6999 (tm-30) REVERT: E 347 PHE cc_start: 0.8329 (m-80) cc_final: 0.8069 (m-80) REVERT: E 420 ASP cc_start: 0.8462 (m-30) cc_final: 0.8221 (m-30) outliers start: 13 outliers final: 11 residues processed: 111 average time/residue: 0.0687 time to fit residues: 10.8873 Evaluate side-chains 108 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU 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 444 LEU 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 385 THR Chi-restraints excluded: chain E residue 387 LEU 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: 0.8980 chunk 67 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 57 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.166931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.144313 restraints weight = 22599.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.147148 restraints weight = 25951.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.149375 restraints weight = 8350.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.151395 restraints weight = 5323.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.151345 restraints weight = 3608.016| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6690 Z= 0.124 Angle : 0.682 20.231 9107 Z= 0.324 Chirality : 0.048 0.569 963 Planarity : 0.004 0.035 1172 Dihedral : 4.180 24.096 864 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.87 % Allowed : 19.25 % Favored : 78.88 % 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: 0.43 (0.30), residues: 789 helix: 0.69 (0.27), residues: 397 sheet: -0.19 (0.75), residues: 47 loop : 0.05 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 355 TYR 0.012 0.001 TYR E 508 PHE 0.015 0.001 PHE A 308 TRP 0.027 0.001 TRP A 302 HIS 0.002 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6676) covalent geometry : angle 0.62858 / 0.31 ( 9078) SS BOND : bond 0.00161 / 0.09 ( 7) SS BOND : angle 0.83998 / 0.46 ( 14) hydrogen bonds : bond 0.03518 / 2.24 ( 273) hydrogen bonds : angle 4.80266 / 3.24 ( 769) metal coordination : bond 0.00007 / 0.00 ( 2) link_NAG-ASN : bond 0.00208 / 0.11 ( 5) link_NAG-ASN : angle 6.54912 / 3.34 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1355.60 seconds wall clock time: 24 minutes 12.05 seconds (1452.05 seconds total)