Starting phenix.real_space_refine on Thu Jul 24 19:32:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vx4_32168/07_2025/7vx4_32168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx4_32168/07_2025/7vx4_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_32168/07_2025/7vx4_32168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx4_32168/07_2025/7vx4_32168.map" model { file = "/net/cci-nas-00/data/ceres_data/7vx4_32168/07_2025/7vx4_32168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx4_32168/07_2025/7vx4_32168.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6493 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1545 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1539 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1576 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.09, per 1000 atoms: 1.25 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: 1.61 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.63 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: 1.70 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2081 1.34 - 1.46: 1727 1.46 - 1.58: 2810 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6676 Sorted by residual: bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.38e+00 ... (remaining 6671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8930 1.97 - 3.95: 135 3.95 - 5.92: 12 5.92 - 7.90: 0 7.90 - 9.87: 1 Bond angle restraints: 9078 Sorted by residual: angle pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta sigma weight residual 121.98 131.85 -9.87 3.11e+00 1.03e-01 1.01e+01 angle pdb=" N TYR E 505 " pdb=" CA TYR E 505 " pdb=" C TYR E 505 " ideal model delta sigma weight residual 111.36 114.77 -3.41 1.09e+00 8.42e-01 9.78e+00 angle pdb=" N ASP A 136 " pdb=" CA ASP A 136 " pdb=" C ASP A 136 " ideal model delta sigma weight residual 111.07 114.15 -3.08 1.07e+00 8.73e-01 8.31e+00 angle pdb=" N VAL A 293 " pdb=" CA VAL A 293 " pdb=" C VAL A 293 " ideal model delta sigma weight residual 112.83 110.26 2.57 9.90e-01 1.02e+00 6.75e+00 angle pdb=" C LYS A 363 " pdb=" N VAL A 364 " pdb=" CA VAL A 364 " ideal model delta sigma weight residual 122.43 119.17 3.26 1.26e+00 6.30e-01 6.71e+00 ... (remaining 9073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 3883 16.02 - 32.05: 77 32.05 - 48.07: 33 48.07 - 64.09: 8 64.09 - 80.12: 3 Dihedral angle restraints: 4004 sinusoidal: 1675 harmonic: 2329 Sorted by residual: dihedral pdb=" CA PHE E 497 " pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N GLY A 147 " pdb=" CA GLY A 147 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA E 352 " pdb=" C ALA E 352 " pdb=" N TRP E 353 " pdb=" CA TRP E 353 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 584 0.030 - 0.061: 242 0.061 - 0.091: 91 0.091 - 0.121: 42 0.121 - 0.151: 4 Chirality restraints: 963 Sorted by residual: chirality pdb=" C1 NAG E1301 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E1301 " pdb=" O5 NAG E1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA TYR E 505 " pdb=" N TYR E 505 " pdb=" C TYR E 505 " pdb=" CB TYR E 505 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 960 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 504 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C GLY E 504 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY E 504 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR E 505 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 611 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 612 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 612 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 612 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.012 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR E 495 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.001 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 87 2.65 - 3.21: 6043 3.21 - 3.77: 9658 3.77 - 4.34: 13646 4.34 - 4.90: 22092 Nonbonded interactions: 51526 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.082 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.189 2.230 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.225 3.040 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.234 3.040 ... (remaining 51521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 6690 Z= 0.165 Angle : 0.629 9.874 9107 Z= 0.393 Chirality : 0.042 0.151 963 Planarity : 0.004 0.038 1172 Dihedral : 8.878 80.115 2491 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP A 302 HIS 0.003 0.001 HIS A 34 PHE 0.020 0.002 PHE E 497 TYR 0.025 0.001 TYR E 495 ARG 0.006 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 5) link_NAG-ASN : angle 1.14301 ( 15) hydrogen bonds : bond 0.28753 ( 273) hydrogen bonds : angle 9.28745 ( 769) metal coordination : bond 0.11493 ( 2) SS BOND : bond 0.00151 ( 7) SS BOND : angle 0.95740 ( 14) covalent geometry : bond 0.00280 ( 6676) covalent geometry : angle 0.62704 ( 9078) *********************** 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 : 0.647 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: 0.7400 (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: 0.8043 (t80) REVERT: A 295 ASP cc_start: 0.7665 (m-30) cc_final: 0.7324 (t70) REVERT: A 442 GLN cc_start: 0.8439 (mm110) cc_final: 0.8125 (mt0) REVERT: A 484 ILE cc_start: 0.8329 (mt) cc_final: 0.8079 (mt) REVERT: A 559 ARG cc_start: 0.8692 (ptm-80) cc_final: 0.8191 (ttp-110) REVERT: A 584 LEU cc_start: 0.7155 (tp) cc_final: 0.6871 (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: 0.7284 (mt) REVERT: E 356 LYS cc_start: 0.8642 (tttp) cc_final: 0.8400 (ttpp) REVERT: E 422 ASN cc_start: 0.7524 (m-40) cc_final: 0.7095 (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: 0.2115 time to fit residues: 63.2084 Evaluate side-chains 127 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.0870 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 61 ASN A 524 GLN A 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.176236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.148276 restraints weight = 17147.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.153526 restraints weight = 21868.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.156218 restraints weight = 7409.450| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4093 r_free = 0.4093 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3305 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= 0.154 Angle : 0.651 9.523 9107 Z= 0.339 Chirality : 0.045 0.166 963 Planarity : 0.005 0.032 1172 Dihedral : 5.616 43.426 969 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.45 % Allowed : 10.78 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.28), residues: 789 helix: -0.63 (0.24), residues: 380 sheet: -0.10 (0.65), residues: 44 loop : 0.09 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 594 HIS 0.003 0.001 HIS A 34 PHE 0.029 0.002 PHE A 308 TYR 0.024 0.002 TYR E 495 ARG 0.007 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 5) link_NAG-ASN : angle 1.91561 ( 15) hydrogen bonds : bond 0.05098 ( 273) hydrogen bonds : angle 5.47506 ( 769) metal coordination : bond 0.00369 ( 2) SS BOND : bond 0.00294 ( 7) SS BOND : angle 1.40159 ( 14) covalent geometry : bond 0.00337 ( 6676) covalent geometry : angle 0.64467 ( 9078) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7813 (mttt) cc_final: 0.7593 (mtpt) REVERT: A 152 MET cc_start: 0.5922 (mmt) cc_final: 0.5694 (mmt) REVERT: A 222 LEU cc_start: 0.8111 (tp) cc_final: 0.7658 (tp) REVERT: A 295 ASP cc_start: 0.7554 (m-30) cc_final: 0.7220 (t70) REVERT: A 299 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7420 (t0) outliers start: 22 outliers final: 14 residues processed: 147 average time/residue: 0.1708 time to fit residues: 34.4177 Evaluate side-chains 120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 256 ILE 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 70 optimal weight: 0.0470 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 598 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.203289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.171331 restraints weight = 25468.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.176907 restraints weight = 24326.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.182079 restraints weight = 7599.096| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6690 Z= 0.129 Angle : 0.604 9.272 9107 Z= 0.310 Chirality : 0.043 0.202 963 Planarity : 0.004 0.034 1172 Dihedral : 5.063 34.040 969 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.59 % Allowed : 12.93 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.28), residues: 789 helix: -0.05 (0.25), residues: 390 sheet: -0.04 (0.65), residues: 45 loop : 0.14 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 594 HIS 0.003 0.001 HIS A 34 PHE 0.022 0.002 PHE E 497 TYR 0.020 0.001 TYR E 495 ARG 0.006 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 5) link_NAG-ASN : angle 1.34649 ( 15) hydrogen bonds : bond 0.04433 ( 273) hydrogen bonds : angle 5.14750 ( 769) metal coordination : bond 0.00008 ( 2) SS BOND : bond 0.00225 ( 7) SS BOND : angle 1.08923 ( 14) covalent geometry : bond 0.00284 ( 6676) covalent geometry : angle 0.60049 ( 9078) *********************** 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 131 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8236 (mttt) cc_final: 0.7885 (mtpt) REVERT: A 222 LEU cc_start: 0.7994 (tp) cc_final: 0.7652 (tp) REVERT: A 295 ASP cc_start: 0.7746 (m-30) cc_final: 0.7210 (t0) REVERT: A 323 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7442 (mmm) REVERT: E 438 SER cc_start: 0.9157 (p) cc_final: 0.8930 (p) outliers start: 16 outliers final: 10 residues processed: 124 average time/residue: 0.1581 time to fit residues: 27.7012 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 : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 256 ILE 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 385 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 277 ASN A 373 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 598 GLN A 599 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.167104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135430 restraints weight = 17875.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.141352 restraints weight = 21151.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.143557 restraints weight = 6733.756| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6690 Z= 0.159 Angle : 0.620 7.775 9107 Z= 0.316 Chirality : 0.045 0.206 963 Planarity : 0.004 0.036 1172 Dihedral : 4.935 33.682 969 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.74 % Allowed : 12.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 789 helix: 0.13 (0.26), residues: 397 sheet: 0.00 (0.68), residues: 45 loop : 0.07 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 594 HIS 0.004 0.001 HIS A 34 PHE 0.022 0.002 PHE E 497 TYR 0.019 0.002 TYR E 495 ARG 0.004 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 5) link_NAG-ASN : angle 1.88970 ( 15) hydrogen bonds : bond 0.04291 ( 273) hydrogen bonds : angle 5.04309 ( 769) metal coordination : bond 0.00010 ( 2) SS BOND : bond 0.00295 ( 7) SS BOND : angle 1.10298 ( 14) covalent geometry : bond 0.00367 ( 6676) covalent geometry : angle 0.61484 ( 9078) *********************** 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 126 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8200 (mttt) cc_final: 0.7903 (mtpt) REVERT: A 62 MET cc_start: 0.8695 (tmm) cc_final: 0.8190 (tpp) REVERT: A 222 LEU cc_start: 0.8067 (tp) cc_final: 0.7732 (tp) REVERT: A 291 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5606 (tp) REVERT: A 295 ASP cc_start: 0.7817 (m-30) cc_final: 0.7277 (t0) REVERT: A 474 MET cc_start: 0.8197 (mmp) cc_final: 0.7917 (mmp) REVERT: A 598 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7359 (mp-120) REVERT: E 422 ASN cc_start: 0.8535 (m-40) cc_final: 0.8018 (p0) outliers start: 24 outliers final: 14 residues processed: 119 average time/residue: 0.1496 time to fit residues: 25.4987 Evaluate side-chains 108 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 159 ASN Chi-restraints excluded: chain A residue 291 ILE 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 468 ILE Chi-restraints excluded: chain A residue 598 GLN 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 13 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 598 GLN 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 = 0.165488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135208 restraints weight = 11006.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136132 restraints weight = 10854.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.137552 restraints weight = 9523.344| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4871 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= 0.155 Angle : 0.597 8.412 9107 Z= 0.306 Chirality : 0.045 0.207 963 Planarity : 0.004 0.037 1172 Dihedral : 4.780 31.194 969 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.02 % Allowed : 13.79 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 789 helix: 0.35 (0.26), residues: 396 sheet: -0.04 (0.69), residues: 49 loop : 0.09 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 594 HIS 0.002 0.001 HIS A 505 PHE 0.019 0.002 PHE E 497 TYR 0.017 0.002 TYR E 495 ARG 0.004 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 5) link_NAG-ASN : angle 1.48979 ( 15) hydrogen bonds : bond 0.04142 ( 273) hydrogen bonds : angle 5.00466 ( 769) metal coordination : bond 0.00058 ( 2) SS BOND : bond 0.00301 ( 7) SS BOND : angle 0.99920 ( 14) covalent geometry : bond 0.00356 ( 6676) covalent geometry : angle 0.59393 ( 9078) *********************** 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 117 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8248 (mttt) cc_final: 0.7978 (mtpt) REVERT: A 62 MET cc_start: 0.8736 (tmm) cc_final: 0.8052 (tpt) REVERT: A 222 LEU cc_start: 0.8075 (tp) cc_final: 0.7825 (tt) REVERT: A 291 ILE cc_start: 0.6169 (OUTLIER) cc_final: 0.5540 (tp) REVERT: A 295 ASP cc_start: 0.7808 (m-30) cc_final: 0.7453 (t0) REVERT: A 305 GLN cc_start: 0.7909 (tp40) cc_final: 0.7380 (tp40) REVERT: A 474 MET cc_start: 0.8237 (mmp) cc_final: 0.7919 (mmp) REVERT: A 482 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7606 (mtp85) REVERT: A 598 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7312 (mp-120) outliers start: 19 outliers final: 13 residues processed: 113 average time/residue: 0.1630 time to fit residues: 25.5554 Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 291 ILE 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 444 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 598 GLN 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 3 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 417 HIS A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.166185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133869 restraints weight = 15663.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.140341 restraints weight = 18444.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.141663 restraints weight = 6710.286| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6690 Z= 0.136 Angle : 0.578 9.010 9107 Z= 0.296 Chirality : 0.044 0.201 963 Planarity : 0.004 0.037 1172 Dihedral : 4.597 30.396 969 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.02 % Allowed : 15.52 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.29), residues: 789 helix: 0.44 (0.26), residues: 399 sheet: -0.12 (0.70), residues: 49 loop : 0.07 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 302 HIS 0.003 0.001 HIS A 505 PHE 0.016 0.002 PHE E 497 TYR 0.017 0.001 TYR E 508 ARG 0.003 0.000 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 5) link_NAG-ASN : angle 1.33742 ( 15) hydrogen bonds : bond 0.03902 ( 273) hydrogen bonds : angle 4.96850 ( 769) metal coordination : bond 0.00028 ( 2) SS BOND : bond 0.00239 ( 7) SS BOND : angle 0.91967 ( 14) covalent geometry : bond 0.00308 ( 6676) covalent geometry : angle 0.57539 ( 9078) *********************** 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 119 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8171 (mttt) cc_final: 0.7911 (mtpt) REVERT: A 62 MET cc_start: 0.8723 (tmm) cc_final: 0.8147 (tpt) REVERT: A 222 LEU cc_start: 0.8080 (tp) cc_final: 0.7846 (tp) REVERT: A 295 ASP cc_start: 0.7810 (m-30) cc_final: 0.7557 (t0) REVERT: A 474 MET cc_start: 0.8266 (mmp) cc_final: 0.7955 (mmp) REVERT: A 482 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7592 (mtp85) REVERT: E 422 ASN cc_start: 0.8599 (m-40) cc_final: 0.8030 (p0) outliers start: 19 outliers final: 15 residues processed: 113 average time/residue: 0.1914 time to fit residues: 29.6202 Evaluate side-chains 111 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 358 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 0.0060 chunk 46 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 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 = 0.3775 r_free = 0.3775 target = 0.166709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.137170 restraints weight = 10906.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136868 restraints weight = 10248.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.138838 restraints weight = 10034.078| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5198 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= 0.114 Angle : 0.560 9.230 9107 Z= 0.284 Chirality : 0.043 0.199 963 Planarity : 0.003 0.037 1172 Dihedral : 4.372 29.563 969 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.73 % Allowed : 15.80 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 789 helix: 0.56 (0.26), residues: 401 sheet: -0.14 (0.71), residues: 49 loop : 0.06 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 594 HIS 0.003 0.001 HIS A 505 PHE 0.015 0.001 PHE A 308 TYR 0.013 0.001 TYR E 508 ARG 0.003 0.000 ARG E 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00089 ( 5) link_NAG-ASN : angle 1.26332 ( 15) hydrogen bonds : bond 0.03717 ( 273) hydrogen bonds : angle 4.86144 ( 769) metal coordination : bond 0.00024 ( 2) SS BOND : bond 0.00179 ( 7) SS BOND : angle 0.83858 ( 14) covalent geometry : bond 0.00250 ( 6676) covalent geometry : angle 0.55728 ( 9078) *********************** 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 120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.806 Fit side-chains REVERT: A 26 LYS cc_start: 0.8195 (mttt) cc_final: 0.7949 (mtpt) REVERT: A 62 MET cc_start: 0.8809 (tmm) cc_final: 0.8136 (tpt) REVERT: A 100 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7912 (tt) REVERT: A 190 MET cc_start: 0.6778 (ttt) cc_final: 0.6443 (ttt) REVERT: A 222 LEU cc_start: 0.8012 (tp) cc_final: 0.7779 (tp) REVERT: A 291 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6160 (tp) REVERT: A 295 ASP cc_start: 0.7825 (m-30) cc_final: 0.7459 (t0) REVERT: A 424 LEU cc_start: 0.7664 (mp) cc_final: 0.7214 (mp) REVERT: A 474 MET cc_start: 0.8099 (mmp) cc_final: 0.7787 (mmp) REVERT: A 482 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7601 (mtp85) REVERT: A 598 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6644 (tm-30) REVERT: E 422 ASN cc_start: 0.8556 (m-40) cc_final: 0.8121 (p0) outliers start: 17 outliers final: 13 residues processed: 117 average time/residue: 0.1750 time to fit residues: 28.3811 Evaluate side-chains 111 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 358 ILE 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 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 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.165338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135482 restraints weight = 12677.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.137409 restraints weight = 12476.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.138881 restraints weight = 8780.574| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5395 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= 0.134 Angle : 0.580 9.206 9107 Z= 0.296 Chirality : 0.044 0.219 963 Planarity : 0.004 0.038 1172 Dihedral : 4.402 28.953 969 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.30 % Allowed : 16.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.29), residues: 789 helix: 0.62 (0.27), residues: 398 sheet: -0.17 (0.72), residues: 49 loop : 0.06 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 302 HIS 0.003 0.001 HIS A 505 PHE 0.017 0.002 PHE A 308 TYR 0.013 0.001 TYR E 453 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 5) link_NAG-ASN : angle 1.88466 ( 15) hydrogen bonds : bond 0.03845 ( 273) hydrogen bonds : angle 4.86885 ( 769) metal coordination : bond 0.00019 ( 2) SS BOND : bond 0.00249 ( 7) SS BOND : angle 0.86529 ( 14) covalent geometry : bond 0.00304 ( 6676) covalent geometry : angle 0.57471 ( 9078) *********************** 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 120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.656 Fit side-chains REVERT: A 26 LYS cc_start: 0.8166 (mttt) cc_final: 0.7920 (mtpt) REVERT: A 62 MET cc_start: 0.8758 (tmm) cc_final: 0.8163 (tpt) REVERT: A 100 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7938 (tt) REVERT: A 222 LEU cc_start: 0.8116 (tp) cc_final: 0.7911 (tt) REVERT: A 291 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.6311 (tp) REVERT: A 295 ASP cc_start: 0.7711 (m-30) cc_final: 0.7418 (t0) REVERT: A 353 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8344 (ttpt) REVERT: A 424 LEU cc_start: 0.7665 (mp) cc_final: 0.7238 (mp) REVERT: A 598 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: E 422 ASN cc_start: 0.8564 (m-40) cc_final: 0.8118 (p0) outliers start: 21 outliers final: 17 residues processed: 114 average time/residue: 0.2378 time to fit residues: 36.8540 Evaluate side-chains 113 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 358 ILE 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 564 GLU Chi-restraints excluded: chain A residue 598 GLN 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 466 ARG 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 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.163767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.131416 restraints weight = 18269.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.136678 restraints weight = 21109.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.138597 restraints weight = 7416.905| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6690 Z= 0.147 Angle : 0.653 16.347 9107 Z= 0.324 Chirality : 0.047 0.375 963 Planarity : 0.004 0.050 1172 Dihedral : 5.749 55.256 969 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.74 % Allowed : 16.38 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.30), residues: 789 helix: 0.65 (0.27), residues: 398 sheet: -0.15 (0.73), residues: 47 loop : -0.04 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 302 HIS 0.002 0.001 HIS A 535 PHE 0.016 0.002 PHE A 308 TYR 0.021 0.002 TYR A 515 ARG 0.005 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 5) link_NAG-ASN : angle 5.38037 ( 15) hydrogen bonds : bond 0.03802 ( 273) hydrogen bonds : angle 4.86059 ( 769) metal coordination : bond 0.00013 ( 2) SS BOND : bond 0.00274 ( 7) SS BOND : angle 0.89814 ( 14) covalent geometry : bond 0.00336 ( 6676) covalent geometry : angle 0.61582 ( 9078) *********************** 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 116 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8233 (mttt) cc_final: 0.7973 (mtpt) REVERT: A 62 MET cc_start: 0.8798 (tmm) cc_final: 0.8179 (tpt) REVERT: A 100 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7967 (tt) REVERT: A 222 LEU cc_start: 0.8115 (tp) cc_final: 0.7909 (tt) REVERT: A 291 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6238 (tp) REVERT: A 295 ASP cc_start: 0.7777 (m-30) cc_final: 0.7505 (t0) REVERT: A 424 LEU cc_start: 0.7660 (mp) cc_final: 0.7265 (mp) REVERT: A 503 LEU cc_start: 0.8593 (tp) cc_final: 0.8365 (tp) outliers start: 24 outliers final: 17 residues processed: 110 average time/residue: 0.1778 time to fit residues: 26.7502 Evaluate side-chains 109 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 291 ILE Chi-restraints excluded: chain A residue 317 SER 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 444 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 598 GLN 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 466 ARG Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.167400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.136182 restraints weight = 13882.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.140498 restraints weight = 16977.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.141936 restraints weight = 9137.908| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6690 Z= 0.165 Angle : 0.665 15.302 9107 Z= 0.328 Chirality : 0.050 0.576 963 Planarity : 0.004 0.041 1172 Dihedral : 5.354 55.093 969 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.02 % Allowed : 16.95 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 789 helix: 0.62 (0.27), residues: 396 sheet: -0.42 (0.72), residues: 48 loop : -0.12 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 302 HIS 0.002 0.001 HIS A 239 PHE 0.018 0.002 PHE E 429 TYR 0.018 0.002 TYR A 515 ARG 0.006 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 5) link_NAG-ASN : angle 5.39137 ( 15) hydrogen bonds : bond 0.03847 ( 273) hydrogen bonds : angle 4.94215 ( 769) metal coordination : bond 0.00015 ( 2) SS BOND : bond 0.00320 ( 7) SS BOND : angle 0.96236 ( 14) covalent geometry : bond 0.00384 ( 6676) covalent geometry : angle 0.62834 ( 9078) ********************** 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 114 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8267 (mttt) cc_final: 0.8013 (mtpt) REVERT: A 62 MET cc_start: 0.8733 (tmm) cc_final: 0.8064 (tpt) REVERT: A 100 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8020 (tt) REVERT: A 291 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.6184 (tp) REVERT: A 295 ASP cc_start: 0.7763 (m-30) cc_final: 0.7509 (t0) REVERT: A 312 GLU cc_start: 0.7587 (tp30) cc_final: 0.7240 (tp30) REVERT: A 424 LEU cc_start: 0.7661 (mp) cc_final: 0.7259 (mp) REVERT: A 556 ASN cc_start: 0.8571 (m-40) cc_final: 0.8068 (m110) REVERT: E 420 ASP cc_start: 0.8317 (m-30) cc_final: 0.8111 (m-30) outliers start: 19 outliers final: 17 residues processed: 109 average time/residue: 0.1806 time to fit residues: 27.0474 Evaluate side-chains 112 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 291 ILE Chi-restraints excluded: chain A residue 317 SER 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 444 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 598 GLN 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 466 ARG Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 68 optimal weight: 0.0770 chunk 4 optimal weight: 0.2980 chunk 32 optimal weight: 0.0040 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 0.0020 chunk 73 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.1158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.180894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.151606 restraints weight = 13972.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.156396 restraints weight = 17596.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.158362 restraints weight = 8656.489| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6690 Z= 0.108 Angle : 0.626 14.079 9107 Z= 0.305 Chirality : 0.044 0.387 963 Planarity : 0.004 0.037 1172 Dihedral : 4.793 49.169 969 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.30 % Allowed : 17.82 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 789 helix: 0.65 (0.27), residues: 398 sheet: -0.17 (0.74), residues: 47 loop : 0.03 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 302 HIS 0.002 0.000 HIS A 535 PHE 0.015 0.001 PHE A 308 TYR 0.017 0.001 TYR A 515 ARG 0.008 0.001 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 5) link_NAG-ASN : angle 4.87730 ( 15) hydrogen bonds : bond 0.03526 ( 273) hydrogen bonds : angle 4.82270 ( 769) metal coordination : bond 0.00032 ( 2) SS BOND : bond 0.00137 ( 7) SS BOND : angle 0.81771 ( 14) covalent geometry : bond 0.00227 ( 6676) covalent geometry : angle 0.59375 ( 9078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.49 seconds wall clock time: 47 minutes 44.67 seconds (2864.67 seconds total)