Starting phenix.real_space_refine on Tue May 13 12:43:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y18_38827/05_2025/8y18_38827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y18_38827/05_2025/8y18_38827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y18_38827/05_2025/8y18_38827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y18_38827/05_2025/8y18_38827.map" model { file = "/net/cci-nas-00/data/ceres_data/8y18_38827/05_2025/8y18_38827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y18_38827/05_2025/8y18_38827.cif" } resolution = 3.04 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= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4869 atoms to isotropic. 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 36 5.16 5 C 4198 2.51 5 N 1070 2.21 5 O 1260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6565 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1491 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 11, 'TRANS': 172} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" 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: 9.97, per 1000 atoms: 1.52 Number of scatterers: 6565 At special positions: 0 Unit cell: (92.46, 76.59, 112.47, 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 36 16.00 O 1260 8.00 N 1070 7.00 C 4198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 432 " " NAG B1301 " - " ASN B 354 " " NAG C 1 " - " ASN A 90 " " NAG D 1 " - " ASN A 322 " " NAG E 1 " - " ASN A 546 " " NAG F 1 " - " ASN A 103 " " NAG G 1 " - " ASN B 343 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1474 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 55.6% alpha, 4.6% 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: 4.068A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.536A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 83 removed outlier: 3.836A pdb=" N TYR A 83 " --> pdb=" O ALA A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.917A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.951A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 194 removed outlier: 3.740A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 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 248 removed outlier: 4.092A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' 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 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.581A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.754A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.870A 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 413 removed outlier: 3.627A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 4.241A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 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: 3.796A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (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: 3.734A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.562A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.766A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.531A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.761A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.819A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 442 removed outlier: 3.546A pdb=" N ASP B 442 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 442' 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: 6.467A 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: 6.111A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.564A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.024A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 435 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 269 hydrogen bonds defined for protein. 758 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: 1.63 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2066 1.34 - 1.46: 1659 1.46 - 1.58: 2970 1.58 - 1.70: 1 1.70 - 1.81: 57 Bond restraints: 6753 Sorted by residual: bond pdb=" N ASN B 354 " pdb=" CA ASN B 354 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.34e-02 5.57e+03 5.22e+00 bond pdb=" N ASN A 322 " pdb=" CA ASN A 322 " ideal model delta sigma weight residual 1.455 1.478 -0.022 1.09e-02 8.42e+03 4.19e+00 bond pdb=" CA GLN A 89 " pdb=" CB GLN A 89 " ideal model delta sigma weight residual 1.531 1.592 -0.062 3.12e-02 1.03e+03 3.90e+00 bond pdb=" N ALA B 344 " pdb=" CA ALA B 344 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.14e-02 7.69e+03 3.66e+00 bond pdb=" C2 BMA D 3 " pdb=" C3 BMA D 3 " ideal model delta sigma weight residual 1.544 1.507 0.037 2.00e-02 2.50e+03 3.39e+00 ... (remaining 6748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 8803 1.39 - 2.78: 268 2.78 - 4.18: 81 4.18 - 5.57: 22 5.57 - 6.96: 3 Bond angle restraints: 9177 Sorted by residual: angle pdb=" N PHE B 342 " pdb=" CA PHE B 342 " pdb=" C PHE B 342 " ideal model delta sigma weight residual 112.88 107.82 5.06 1.29e+00 6.01e-01 1.54e+01 angle pdb=" O ALA B 352 " pdb=" C ALA B 352 " pdb=" N TRP B 353 " ideal model delta sigma weight residual 122.59 127.13 -4.54 1.33e+00 5.65e-01 1.17e+01 angle pdb=" C PRO A 321 " pdb=" N ASN A 322 " pdb=" CA ASN A 322 " ideal model delta sigma weight residual 122.15 116.47 5.68 1.74e+00 3.30e-01 1.07e+01 angle pdb=" CA ASN B 343 " pdb=" C ASN B 343 " pdb=" O ASN B 343 " ideal model delta sigma weight residual 121.67 118.85 2.82 9.30e-01 1.16e+00 9.19e+00 angle pdb=" C ASN A 322 " pdb=" CA ASN A 322 " pdb=" CB ASN A 322 " ideal model delta sigma weight residual 114.16 107.20 6.96 2.31e+00 1.87e-01 9.08e+00 ... (remaining 9172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 3853 21.23 - 42.46: 250 42.46 - 63.70: 35 63.70 - 84.93: 21 84.93 - 106.16: 10 Dihedral angle restraints: 4169 sinusoidal: 1872 harmonic: 2297 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -167.96 81.96 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -17.53 -68.47 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -117.68 31.68 1 1.00e+01 1.00e-02 1.43e+01 ... (remaining 4166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 980 0.166 - 0.332: 12 0.332 - 0.499: 0 0.499 - 0.665: 2 0.665 - 0.831: 1 Chirality restraints: 995 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.71e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.08e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.71e+02 ... (remaining 992 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.298 2.00e-02 2.50e+03 2.57e-01 8.26e+02 pdb=" C7 NAG G 2 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.155 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.456 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.233 2.00e-02 2.50e+03 1.96e-01 4.82e+02 pdb=" C7 NAG G 1 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.329 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.157 2.00e-02 2.50e+03 1.32e-01 2.17e+02 pdb=" C7 NAG B1301 " 0.042 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.217 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " 0.012 2.00e-02 2.50e+03 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 79 2.66 - 3.22: 5992 3.22 - 3.78: 9533 3.78 - 4.34: 12683 4.34 - 4.90: 20686 Nonbonded interactions: 48973 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.100 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.108 2.230 nonbonded pdb=" NE2 HIS A 374 " pdb=" OE1 GLU A 402 " model vdw 2.231 3.120 nonbonded pdb=" NE2 GLN B 474 " pdb=" O GLY B 476 " model vdw 2.274 3.120 nonbonded pdb=" OD1 ASN A 134 " pdb=" ND2 ASN A 137 " model vdw 2.275 3.120 ... (remaining 48968 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 18.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.930 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 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 : 0.005 0.207 6776 Z= 0.233 Angle : 0.828 17.801 9234 Z= 0.384 Chirality : 0.063 0.831 995 Planarity : 0.013 0.257 1166 Dihedral : 15.606 106.161 2677 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.31), residues: 777 helix: 1.82 (0.29), residues: 344 sheet: -1.32 (0.88), residues: 26 loop : -1.23 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 203 HIS 0.012 0.001 HIS A 401 PHE 0.012 0.001 PHE B 338 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.01470 ( 8) link_NAG-ASN : angle 6.35494 ( 24) link_BETA1-4 : bond 0.04597 ( 7) link_BETA1-4 : angle 8.35650 ( 21) hydrogen bonds : bond 0.16932 ( 269) hydrogen bonds : angle 5.28247 ( 758) metal coordination : bond 0.20497 ( 2) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.64217 ( 12) covalent geometry : bond 0.00358 ( 6753) covalent geometry : angle 0.65084 ( 9177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 THR cc_start: 0.8241 (p) cc_final: 0.7924 (p) REVERT: B 492 LEU cc_start: 0.7615 (mt) cc_final: 0.7133 (mt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2184 time to fit residues: 35.8957 Evaluate side-chains 63 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.062253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.049317 restraints weight = 71454.467| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 7.12 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6776 Z= 0.159 Angle : 0.725 9.125 9234 Z= 0.354 Chirality : 0.046 0.370 995 Planarity : 0.004 0.033 1166 Dihedral : 9.899 68.040 1160 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.02 % Allowed : 10.04 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.12 (0.31), residues: 777 helix: 1.52 (0.28), residues: 358 sheet: -1.17 (0.95), residues: 31 loop : -1.25 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 606 HIS 0.006 0.001 HIS A 378 PHE 0.016 0.001 PHE B 515 TYR 0.019 0.002 TYR A 50 ARG 0.008 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 8) link_NAG-ASN : angle 3.56668 ( 24) link_BETA1-4 : bond 0.01269 ( 7) link_BETA1-4 : angle 3.22650 ( 21) hydrogen bonds : bond 0.05332 ( 269) hydrogen bonds : angle 4.54694 ( 758) metal coordination : bond 0.00941 ( 2) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.66096 ( 12) covalent geometry : bond 0.00356 ( 6753) covalent geometry : angle 0.68634 ( 9177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.1978 time to fit residues: 18.1971 Evaluate side-chains 51 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 101 GLN A 401 HIS A 508 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.057970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.045595 restraints weight = 50673.073| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 5.66 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6776 Z= 0.231 Angle : 0.756 8.976 9234 Z= 0.375 Chirality : 0.046 0.327 995 Planarity : 0.005 0.047 1166 Dihedral : 7.560 57.960 1160 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.75 % Allowed : 11.35 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.08 (0.31), residues: 777 helix: 1.28 (0.28), residues: 358 sheet: -1.74 (0.83), residues: 36 loop : -1.21 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 610 HIS 0.009 0.002 HIS A 378 PHE 0.025 0.002 PHE A 230 TYR 0.018 0.002 TYR A 515 ARG 0.005 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 8) link_NAG-ASN : angle 3.05667 ( 24) link_BETA1-4 : bond 0.01137 ( 7) link_BETA1-4 : angle 3.01224 ( 21) hydrogen bonds : bond 0.05492 ( 269) hydrogen bonds : angle 4.51263 ( 758) metal coordination : bond 0.00335 ( 2) SS BOND : bond 0.00392 ( 6) SS BOND : angle 1.04912 ( 12) covalent geometry : bond 0.00513 ( 6753) covalent geometry : angle 0.72740 ( 9177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 455 MET cc_start: 0.8352 (tmm) cc_final: 0.7980 (tmm) REVERT: A 480 MET cc_start: 0.9251 (mtp) cc_final: 0.9001 (mtp) outliers start: 12 outliers final: 7 residues processed: 56 average time/residue: 0.1738 time to fit residues: 14.1996 Evaluate side-chains 50 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 37 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.058613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.046304 restraints weight = 52332.832| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 5.81 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6776 Z= 0.126 Angle : 0.653 9.472 9234 Z= 0.315 Chirality : 0.043 0.332 995 Planarity : 0.004 0.031 1166 Dihedral : 6.642 55.114 1160 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.16 % Allowed : 11.94 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.19 (0.31), residues: 777 helix: 1.56 (0.28), residues: 358 sheet: -1.21 (0.87), residues: 31 loop : -1.17 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 610 HIS 0.005 0.001 HIS A 241 PHE 0.018 0.001 PHE B 456 TYR 0.013 0.001 TYR A 50 ARG 0.003 0.000 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 8) link_NAG-ASN : angle 2.96535 ( 24) link_BETA1-4 : bond 0.01218 ( 7) link_BETA1-4 : angle 2.80198 ( 21) hydrogen bonds : bond 0.04553 ( 269) hydrogen bonds : angle 4.33141 ( 758) metal coordination : bond 0.00197 ( 2) SS BOND : bond 0.00352 ( 6) SS BOND : angle 3.07991 ( 12) covalent geometry : bond 0.00274 ( 6753) covalent geometry : angle 0.61285 ( 9177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.8883 (tp30) cc_final: 0.8448 (tm-30) REVERT: A 376 MET cc_start: 0.9105 (tpp) cc_final: 0.8768 (tpp) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.1445 time to fit residues: 11.1577 Evaluate side-chains 47 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.057908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.046133 restraints weight = 41051.983| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.92 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6776 Z= 0.136 Angle : 0.629 8.256 9234 Z= 0.303 Chirality : 0.043 0.321 995 Planarity : 0.004 0.030 1166 Dihedral : 6.328 54.305 1160 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.31 % Allowed : 12.81 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.19 (0.31), residues: 777 helix: 1.54 (0.28), residues: 362 sheet: -0.99 (0.86), residues: 31 loop : -1.20 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 610 HIS 0.006 0.001 HIS A 241 PHE 0.012 0.001 PHE A 230 TYR 0.013 0.001 TYR A 50 ARG 0.003 0.000 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 8) link_NAG-ASN : angle 2.85014 ( 24) link_BETA1-4 : bond 0.01131 ( 7) link_BETA1-4 : angle 2.61548 ( 21) hydrogen bonds : bond 0.04426 ( 269) hydrogen bonds : angle 4.24664 ( 758) metal coordination : bond 0.00270 ( 2) SS BOND : bond 0.00185 ( 6) SS BOND : angle 2.73256 ( 12) covalent geometry : bond 0.00303 ( 6753) covalent geometry : angle 0.59273 ( 9177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.9214 (mmt) cc_final: 0.8979 (mmp) REVERT: A 189 GLU cc_start: 0.8907 (tp30) cc_final: 0.8574 (tm-30) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.1666 time to fit residues: 12.4782 Evaluate side-chains 45 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 52 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.058142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.045195 restraints weight = 79222.487| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 7.04 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6776 Z= 0.112 Angle : 0.615 8.155 9234 Z= 0.294 Chirality : 0.042 0.326 995 Planarity : 0.003 0.033 1166 Dihedral : 6.167 54.306 1160 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.16 % Allowed : 12.95 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.23 (0.31), residues: 777 helix: 1.46 (0.28), residues: 365 sheet: -0.89 (0.85), residues: 31 loop : -1.09 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 606 HIS 0.004 0.001 HIS A 241 PHE 0.007 0.001 PHE B 456 TYR 0.013 0.001 TYR A 50 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 8) link_NAG-ASN : angle 2.82977 ( 24) link_BETA1-4 : bond 0.01189 ( 7) link_BETA1-4 : angle 2.53718 ( 21) hydrogen bonds : bond 0.04153 ( 269) hydrogen bonds : angle 4.22171 ( 758) metal coordination : bond 0.00147 ( 2) SS BOND : bond 0.00147 ( 6) SS BOND : angle 2.11870 ( 12) covalent geometry : bond 0.00243 ( 6753) covalent geometry : angle 0.58190 ( 9177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.8978 (tp30) cc_final: 0.8691 (tm-30) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.1529 time to fit residues: 10.9325 Evaluate side-chains 41 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.057774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.045630 restraints weight = 51311.516| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 5.59 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6776 Z= 0.120 Angle : 0.637 12.784 9234 Z= 0.307 Chirality : 0.044 0.316 995 Planarity : 0.003 0.030 1166 Dihedral : 6.214 54.525 1160 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.60 % Allowed : 12.81 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.31), residues: 777 helix: 1.51 (0.29), residues: 364 sheet: -0.84 (0.74), residues: 43 loop : -0.90 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 610 HIS 0.009 0.001 HIS A 345 PHE 0.009 0.001 PHE A 230 TYR 0.013 0.001 TYR A 50 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 8) link_NAG-ASN : angle 2.77596 ( 24) link_BETA1-4 : bond 0.01184 ( 7) link_BETA1-4 : angle 2.48806 ( 21) hydrogen bonds : bond 0.04143 ( 269) hydrogen bonds : angle 4.23621 ( 758) metal coordination : bond 0.00172 ( 2) SS BOND : bond 0.00355 ( 6) SS BOND : angle 2.38778 ( 12) covalent geometry : bond 0.00264 ( 6753) covalent geometry : angle 0.60556 ( 9177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.9159 (mmt) cc_final: 0.8922 (mmp) REVERT: A 189 GLU cc_start: 0.8925 (tp30) cc_final: 0.8669 (tm-30) REVERT: A 360 MET cc_start: 0.8601 (mmm) cc_final: 0.8341 (mmm) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.1521 time to fit residues: 11.4465 Evaluate side-chains 45 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 59 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 73 optimal weight: 0.0870 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.057859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.045628 restraints weight = 58280.494| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 6.02 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6776 Z= 0.111 Angle : 0.628 9.722 9234 Z= 0.300 Chirality : 0.043 0.321 995 Planarity : 0.004 0.040 1166 Dihedral : 6.138 54.498 1160 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.02 % Allowed : 13.25 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.50 (0.32), residues: 777 helix: 1.57 (0.29), residues: 366 sheet: -0.78 (0.77), residues: 43 loop : -0.80 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 275 HIS 0.003 0.001 HIS A 241 PHE 0.007 0.001 PHE B 392 TYR 0.013 0.001 TYR A 50 ARG 0.006 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 8) link_NAG-ASN : angle 2.75425 ( 24) link_BETA1-4 : bond 0.01112 ( 7) link_BETA1-4 : angle 2.39898 ( 21) hydrogen bonds : bond 0.03938 ( 269) hydrogen bonds : angle 4.11895 ( 758) metal coordination : bond 0.00130 ( 2) SS BOND : bond 0.00516 ( 6) SS BOND : angle 2.53765 ( 12) covalent geometry : bond 0.00238 ( 6753) covalent geometry : angle 0.59586 ( 9177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.705 Fit side-chains REVERT: A 62 MET cc_start: 0.9156 (mmt) cc_final: 0.8930 (mmp) REVERT: A 189 GLU cc_start: 0.8964 (tp30) cc_final: 0.8708 (tm-30) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 0.1441 time to fit residues: 10.3796 Evaluate side-chains 42 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.056550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.043813 restraints weight = 74661.848| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 6.68 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6776 Z= 0.176 Angle : 0.685 9.559 9234 Z= 0.335 Chirality : 0.044 0.316 995 Planarity : 0.004 0.028 1166 Dihedral : 6.372 54.865 1160 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.31 % Allowed : 13.10 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.42 (0.32), residues: 777 helix: 1.46 (0.29), residues: 367 sheet: -0.72 (0.75), residues: 41 loop : -0.81 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 610 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 230 TYR 0.014 0.002 TYR A 50 ARG 0.009 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 8) link_NAG-ASN : angle 2.81096 ( 24) link_BETA1-4 : bond 0.01065 ( 7) link_BETA1-4 : angle 2.37759 ( 21) hydrogen bonds : bond 0.04434 ( 269) hydrogen bonds : angle 4.32963 ( 758) metal coordination : bond 0.00967 ( 2) SS BOND : bond 0.00270 ( 6) SS BOND : angle 2.54979 ( 12) covalent geometry : bond 0.00395 ( 6753) covalent geometry : angle 0.65551 ( 9177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.736 Fit side-chains REVERT: A 62 MET cc_start: 0.9176 (mmt) cc_final: 0.8958 (mmp) REVERT: A 82 MET cc_start: 0.8010 (ptm) cc_final: 0.7038 (ppp) outliers start: 9 outliers final: 8 residues processed: 44 average time/residue: 0.1289 time to fit residues: 9.0668 Evaluate side-chains 41 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 13 optimal weight: 0.0010 chunk 9 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.057410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.045195 restraints weight = 59980.472| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 6.00 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6776 Z= 0.112 Angle : 0.660 10.789 9234 Z= 0.316 Chirality : 0.044 0.317 995 Planarity : 0.003 0.027 1166 Dihedral : 6.242 54.345 1160 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.87 % Allowed : 13.83 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.49 (0.31), residues: 777 helix: 1.58 (0.29), residues: 363 sheet: -0.52 (0.76), residues: 41 loop : -0.84 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 610 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE A 230 TYR 0.013 0.001 TYR A 50 ARG 0.004 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 8) link_NAG-ASN : angle 2.73861 ( 24) link_BETA1-4 : bond 0.01036 ( 7) link_BETA1-4 : angle 2.25666 ( 21) hydrogen bonds : bond 0.04021 ( 269) hydrogen bonds : angle 4.21190 ( 758) metal coordination : bond 0.00266 ( 2) SS BOND : bond 0.00289 ( 6) SS BOND : angle 2.45409 ( 12) covalent geometry : bond 0.00246 ( 6753) covalent geometry : angle 0.63205 ( 9177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.723 Fit side-chains REVERT: A 82 MET cc_start: 0.7922 (ptm) cc_final: 0.7238 (ppp) REVERT: A 360 MET cc_start: 0.7913 (mmp) cc_final: 0.7429 (mmp) REVERT: A 383 MET cc_start: 0.8888 (pmm) cc_final: 0.8655 (pmm) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.1340 time to fit residues: 8.5072 Evaluate side-chains 39 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 0.0870 chunk 72 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.055776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.043034 restraints weight = 81380.675| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 6.82 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6776 Z= 0.190 Angle : 0.714 10.693 9234 Z= 0.346 Chirality : 0.045 0.320 995 Planarity : 0.004 0.030 1166 Dihedral : 6.589 55.034 1160 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.87 % Allowed : 13.68 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.37 (0.31), residues: 777 helix: 1.43 (0.29), residues: 366 sheet: -1.00 (0.70), residues: 45 loop : -0.79 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 610 HIS 0.006 0.001 HIS A 241 PHE 0.016 0.001 PHE A 230 TYR 0.017 0.002 TYR A 381 ARG 0.003 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 8) link_NAG-ASN : angle 2.82385 ( 24) link_BETA1-4 : bond 0.00987 ( 7) link_BETA1-4 : angle 2.21387 ( 21) hydrogen bonds : bond 0.04811 ( 269) hydrogen bonds : angle 4.45216 ( 758) metal coordination : bond 0.00451 ( 2) SS BOND : bond 0.00370 ( 6) SS BOND : angle 2.58785 ( 12) covalent geometry : bond 0.00427 ( 6753) covalent geometry : angle 0.68688 ( 9177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4159.26 seconds wall clock time: 73 minutes 37.20 seconds (4417.20 seconds total)