Starting phenix.real_space_refine on Thu May 1 05:59:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wsr_37822/05_2025/8wsr_37822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wsr_37822/05_2025/8wsr_37822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wsr_37822/05_2025/8wsr_37822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wsr_37822/05_2025/8wsr_37822.map" model { file = "/net/cci-nas-00/data/ceres_data/8wsr_37822/05_2025/8wsr_37822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wsr_37822/05_2025/8wsr_37822.cif" } resolution = 2.99 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= 0.003 sd= 0.040 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 4891 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 37 5.16 5 C 4135 2.51 5 N 1065 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6475 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1514 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.25, per 1000 atoms: 0.66 Number of scatterers: 6475 At special positions: 0 Unit cell: (75.9, 84.18, 120.75, 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 1237 8.00 N 1065 7.00 C 4135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 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 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A 901 " - " ASN A 103 " " NAG A 902 " - " ASN A 53 " " NAG A 903 " - " ASN A 90 " " NAG A 905 " - " ASN A 432 " " NAG A 906 " - " ASN A 322 " " NAG B 1 " - " ASN A 546 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 820.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 378 " 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 59.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.518A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.967A pdb=" N VAL C 354 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 376 removed outlier: 3.754A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 397 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 488 through 492 removed outlier: 4.009A pdb=" N GLN C 492 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.896A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.771A 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: 3.758A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.840A 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 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.721A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.817A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.598A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 193 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 232 removed outlier: 4.121A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.535A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (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 282 removed outlier: 4.236A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.816A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.698A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.862A 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: 3.901A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.514A 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 431 through 447 removed outlier: 3.578A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 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: 3.597A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.584A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.567A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.802A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.838A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.621A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.667A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.177A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 510 " --> pdb=" O PHE C 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.346A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 350 301 hydrogen bonds defined for protein. 840 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: 1.64 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2062 1.34 - 1.46: 1722 1.46 - 1.59: 2813 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6655 Sorted by residual: bond pdb=" N PRO A 135 " pdb=" CD PRO A 135 " ideal model delta sigma weight residual 1.473 1.393 0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" CA TYR A 83 " pdb=" C TYR A 83 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.26e-02 6.30e+03 2.58e+01 bond pdb=" C TYR A 83 " pdb=" N PRO A 84 " ideal model delta sigma weight residual 1.332 1.388 -0.057 1.30e-02 5.92e+03 1.90e+01 bond pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.28e-02 6.10e+03 1.46e+01 bond pdb=" C ILE A 468 " pdb=" N PRO A 469 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.25e-02 6.40e+03 1.14e+01 ... (remaining 6650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 8824 2.32 - 4.65: 190 4.65 - 6.97: 28 6.97 - 9.29: 3 9.29 - 11.62: 6 Bond angle restraints: 9051 Sorted by residual: angle pdb=" N GLY C 463 " pdb=" CA GLY C 463 " pdb=" C GLY C 463 " ideal model delta sigma weight residual 112.37 100.84 11.53 1.40e+00 5.10e-01 6.78e+01 angle pdb=" N TYR C 460 " pdb=" CA TYR C 460 " pdb=" C TYR C 460 " ideal model delta sigma weight residual 111.24 122.11 -10.87 1.38e+00 5.25e-01 6.20e+01 angle pdb=" N ILE C 459 " pdb=" CA ILE C 459 " pdb=" C ILE C 459 " ideal model delta sigma weight residual 112.17 118.43 -6.26 9.50e-01 1.11e+00 4.35e+01 angle pdb=" C ILE A 468 " pdb=" N PRO A 469 " pdb=" CA PRO A 469 " ideal model delta sigma weight residual 120.21 114.43 5.78 9.60e-01 1.09e+00 3.63e+01 angle pdb=" N GLU A 402 " pdb=" CA GLU A 402 " pdb=" C GLU A 402 " ideal model delta sigma weight residual 111.82 118.50 -6.68 1.16e+00 7.43e-01 3.32e+01 ... (remaining 9046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3438 17.86 - 35.73: 415 35.73 - 53.59: 126 53.59 - 71.46: 30 71.46 - 89.32: 11 Dihedral angle restraints: 4020 sinusoidal: 1704 harmonic: 2316 Sorted by residual: dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 348 " pdb=" CB CYS C 348 " ideal model delta sinusoidal sigma weight residual -86.00 -174.14 88.14 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" N TYR C 460 " pdb=" C TYR C 460 " pdb=" CA TYR C 460 " pdb=" CB TYR C 460 " ideal model delta harmonic sigma weight residual 122.80 142.12 -19.32 0 2.50e+00 1.60e-01 5.97e+01 dihedral pdb=" C TYR C 460 " pdb=" N TYR C 460 " pdb=" CA TYR C 460 " pdb=" CB TYR C 460 " ideal model delta harmonic sigma weight residual -122.60 -139.37 16.77 0 2.50e+00 1.60e-01 4.50e+01 ... (remaining 4017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 950 0.172 - 0.343: 16 0.343 - 0.515: 2 0.515 - 0.686: 0 0.686 - 0.858: 1 Chirality restraints: 969 Sorted by residual: chirality pdb=" CA TYR C 460 " pdb=" N TYR C 460 " pdb=" C TYR C 460 " pdb=" CB TYR C 460 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.84e+01 chirality pdb=" CA GLU A 402 " pdb=" N GLU A 402 " pdb=" C GLU A 402 " pdb=" CB GLU A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 966 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " -0.356 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG A 901 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " -0.139 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 906 " 0.263 2.00e-02 2.50e+03 2.25e-01 6.33e+02 pdb=" C7 NAG A 906 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG A 906 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG A 906 " -0.390 2.00e-02 2.50e+03 pdb=" O7 NAG A 906 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 78 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C THR A 78 " 0.052 2.00e-02 2.50e+03 pdb=" O THR A 78 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 79 " -0.017 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.88: 4 1.88 - 2.63: 59 2.63 - 3.39: 8244 3.39 - 4.14: 13890 4.14 - 4.90: 26230 Nonbonded interactions: 48427 Sorted by model distance: nonbonded pdb=" ND2 ASN A 137 " pdb=" OE2 GLU A 140 " model vdw 1.124 3.120 nonbonded pdb=" O PRO A 135 " pdb=" OD1 ASP A 136 " model vdw 1.291 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 904 " model vdw 1.453 2.230 nonbonded pdb=" ND2 ASN A 137 " pdb=" CD GLU A 140 " model vdw 1.735 3.350 nonbonded pdb=" OD1 ASN A 134 " pdb=" CD PRO A 135 " model vdw 2.046 3.440 ... (remaining 48422 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=1.00 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: 1.090 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 18.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 0.080 6671 Z= 0.280 Angle : 0.839 11.615 9086 Z= 0.500 Chirality : 0.063 0.858 969 Planarity : 0.012 0.305 1164 Dihedral : 17.386 89.319 2513 Min Nonbonded Distance : 1.124 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.45 % Allowed : 22.83 % Favored : 75.72 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.56 % 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: -0.22 (0.29), residues: 785 helix: 0.66 (0.28), residues: 383 sheet: 1.16 (0.68), residues: 44 loop : -1.20 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 PHE 0.017 0.001 PHE A 308 TYR 0.020 0.002 TYR A 183 ARG 0.007 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 6) link_NAG-ASN : angle 3.81410 ( 18) link_BETA1-4 : bond 0.00200 ( 1) link_BETA1-4 : angle 1.19021 ( 3) hydrogen bonds : bond 0.18605 ( 301) hydrogen bonds : angle 6.51435 ( 840) metal coordination : bond 0.00503 ( 2) SS BOND : bond 0.00388 ( 7) SS BOND : angle 1.00353 ( 14) covalent geometry : bond 0.00513 ( 6655) covalent geometry : angle 0.82163 ( 9051) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 129 THR cc_start: 0.8785 (t) cc_final: 0.8570 (p) outliers start: 10 outliers final: 6 residues processed: 160 average time/residue: 1.2574 time to fit residues: 210.5909 Evaluate side-chains 140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 391 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 GLN C 437 ASN C 492 GLN A 34 HIS A 42 GLN A 86 GLN A 102 GLN A 121 ASN A 194 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 340 GLN A 535 HIS A 601 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099840 restraints weight = 9673.361| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.26 r_work: 0.3065 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6671 Z= 0.158 Angle : 0.588 9.357 9086 Z= 0.304 Chirality : 0.044 0.266 969 Planarity : 0.005 0.058 1164 Dihedral : 6.724 55.329 1012 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.32 % Allowed : 22.54 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.30 (0.29), residues: 785 helix: 1.36 (0.27), residues: 385 sheet: 1.21 (0.68), residues: 44 loop : -1.28 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.012 0.001 PHE A 308 TYR 0.015 0.001 TYR A 50 ARG 0.006 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 6) link_NAG-ASN : angle 2.61345 ( 18) link_BETA1-4 : bond 0.00444 ( 1) link_BETA1-4 : angle 1.02873 ( 3) hydrogen bonds : bond 0.06616 ( 301) hydrogen bonds : angle 4.44828 ( 840) metal coordination : bond 0.00191 ( 2) SS BOND : bond 0.00282 ( 7) SS BOND : angle 0.76251 ( 14) covalent geometry : bond 0.00356 ( 6655) covalent geometry : angle 0.57609 ( 9051) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 THR cc_start: 0.8739 (t) cc_final: 0.8402 (p) REVERT: A 184 VAL cc_start: 0.8349 (t) cc_final: 0.8068 (t) REVERT: A 257 SER cc_start: 0.9006 (t) cc_final: 0.8705 (p) REVERT: A 325 GLN cc_start: 0.8450 (mt0) cc_final: 0.8230 (mt0) REVERT: A 360 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8453 (ptm) REVERT: A 376 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8687 (ttt) REVERT: A 430 GLU cc_start: 0.8032 (mp0) cc_final: 0.7810 (mp0) REVERT: A 435 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 574 VAL cc_start: 0.8855 (m) cc_final: 0.8584 (t) REVERT: A 600 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8078 (mtmt) outliers start: 23 outliers final: 8 residues processed: 155 average time/residue: 1.2043 time to fit residues: 195.7331 Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.5980 chunk 5 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 134 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 531 GLN A 601 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097257 restraints weight = 9613.568| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.24 r_work: 0.3037 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6671 Z= 0.200 Angle : 0.581 7.379 9086 Z= 0.302 Chirality : 0.045 0.377 969 Planarity : 0.005 0.054 1164 Dihedral : 6.222 59.193 1007 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.61 % Allowed : 22.40 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.37 (0.29), residues: 785 helix: 1.49 (0.27), residues: 385 sheet: 1.18 (0.67), residues: 44 loop : -1.32 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.007 0.001 HIS A 374 PHE 0.017 0.001 PHE A 308 TYR 0.016 0.002 TYR A 183 ARG 0.007 0.001 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 6) link_NAG-ASN : angle 2.52130 ( 18) link_BETA1-4 : bond 0.00160 ( 1) link_BETA1-4 : angle 1.14718 ( 3) hydrogen bonds : bond 0.07342 ( 301) hydrogen bonds : angle 4.32918 ( 840) metal coordination : bond 0.00533 ( 2) SS BOND : bond 0.00378 ( 7) SS BOND : angle 1.02197 ( 14) covalent geometry : bond 0.00467 ( 6655) covalent geometry : angle 0.56986 ( 9051) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: C 489 VAL cc_start: 0.8762 (p) cc_final: 0.8513 (t) REVERT: A 129 THR cc_start: 0.8816 (t) cc_final: 0.8538 (p) REVERT: A 227 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 257 SER cc_start: 0.8997 (t) cc_final: 0.8705 (p) REVERT: A 325 GLN cc_start: 0.8497 (mt0) cc_final: 0.8263 (tt0) REVERT: A 430 GLU cc_start: 0.7982 (mp0) cc_final: 0.7727 (mp0) REVERT: A 435 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 574 VAL cc_start: 0.8950 (m) cc_final: 0.8664 (t) REVERT: A 600 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8089 (mtmt) outliers start: 25 outliers final: 13 residues processed: 155 average time/residue: 1.2438 time to fit residues: 202.3788 Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100352 restraints weight = 9652.995| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.26 r_work: 0.3078 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6671 Z= 0.130 Angle : 0.513 5.541 9086 Z= 0.270 Chirality : 0.042 0.350 969 Planarity : 0.004 0.052 1164 Dihedral : 6.186 59.761 1007 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.32 % Allowed : 22.25 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.56 (0.29), residues: 785 helix: 1.61 (0.27), residues: 386 sheet: 1.22 (0.67), residues: 44 loop : -1.19 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.010 0.001 PHE A 308 TYR 0.016 0.001 TYR A 50 ARG 0.005 0.000 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 6) link_NAG-ASN : angle 2.29302 ( 18) link_BETA1-4 : bond 0.00452 ( 1) link_BETA1-4 : angle 1.11778 ( 3) hydrogen bonds : bond 0.05750 ( 301) hydrogen bonds : angle 4.17388 ( 840) metal coordination : bond 0.00312 ( 2) SS BOND : bond 0.00297 ( 7) SS BOND : angle 0.77340 ( 14) covalent geometry : bond 0.00289 ( 6655) covalent geometry : angle 0.50257 ( 9051) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8168 (t) cc_final: 0.7953 (p) REVERT: C 489 VAL cc_start: 0.8753 (p) cc_final: 0.8498 (t) REVERT: A 129 THR cc_start: 0.8732 (t) cc_final: 0.8414 (p) REVERT: A 166 GLU cc_start: 0.8044 (tp30) cc_final: 0.7659 (mm-30) REVERT: A 171 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: A 184 VAL cc_start: 0.8315 (t) cc_final: 0.8068 (t) REVERT: A 224 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7759 (mt-10) REVERT: A 227 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: A 257 SER cc_start: 0.8984 (t) cc_final: 0.8689 (p) REVERT: A 325 GLN cc_start: 0.8457 (mt0) cc_final: 0.8250 (tt0) REVERT: A 430 GLU cc_start: 0.7954 (mp0) cc_final: 0.7681 (mp0) REVERT: A 435 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 574 VAL cc_start: 0.8905 (m) cc_final: 0.8698 (t) REVERT: A 600 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8113 (mtmt) outliers start: 23 outliers final: 11 residues processed: 147 average time/residue: 1.2375 time to fit residues: 190.7589 Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098145 restraints weight = 9599.427| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.22 r_work: 0.3029 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6671 Z= 0.209 Angle : 0.557 7.295 9086 Z= 0.293 Chirality : 0.045 0.394 969 Planarity : 0.004 0.052 1164 Dihedral : 5.788 52.325 1005 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.61 % Allowed : 22.83 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.49 (0.29), residues: 785 helix: 1.59 (0.27), residues: 384 sheet: 1.28 (0.67), residues: 44 loop : -1.27 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 423 HIS 0.007 0.001 HIS A 374 PHE 0.017 0.001 PHE A 308 TYR 0.016 0.002 TYR A 385 ARG 0.008 0.001 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 6) link_NAG-ASN : angle 2.50668 ( 18) link_BETA1-4 : bond 0.00379 ( 1) link_BETA1-4 : angle 1.31408 ( 3) hydrogen bonds : bond 0.07213 ( 301) hydrogen bonds : angle 4.25388 ( 840) metal coordination : bond 0.00598 ( 2) SS BOND : bond 0.00299 ( 7) SS BOND : angle 1.02581 ( 14) covalent geometry : bond 0.00492 ( 6655) covalent geometry : angle 0.54476 ( 9051) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: C 470 VAL cc_start: 0.8738 (t) cc_final: 0.8486 (p) REVERT: C 489 VAL cc_start: 0.8792 (p) cc_final: 0.8541 (t) REVERT: A 129 THR cc_start: 0.8814 (t) cc_final: 0.8548 (p) REVERT: A 171 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: A 227 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 257 SER cc_start: 0.8975 (t) cc_final: 0.8675 (p) REVERT: A 269 ASP cc_start: 0.8466 (t0) cc_final: 0.8210 (m-30) REVERT: A 325 GLN cc_start: 0.8510 (mt0) cc_final: 0.8276 (tt0) REVERT: A 430 GLU cc_start: 0.7969 (mp0) cc_final: 0.7722 (mp0) REVERT: A 435 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 574 VAL cc_start: 0.8969 (m) cc_final: 0.8722 (t) REVERT: A 600 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8237 (mtmt) outliers start: 25 outliers final: 14 residues processed: 148 average time/residue: 1.3141 time to fit residues: 203.5281 Evaluate side-chains 148 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100883 restraints weight = 9466.525| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.12 r_work: 0.3084 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6671 Z= 0.132 Angle : 0.502 5.172 9086 Z= 0.265 Chirality : 0.042 0.334 969 Planarity : 0.004 0.051 1164 Dihedral : 5.586 53.343 1005 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.03 % Allowed : 23.27 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.59 (0.30), residues: 785 helix: 1.58 (0.27), residues: 392 sheet: 1.48 (0.65), residues: 43 loop : -1.18 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.010 0.001 PHE A 308 TYR 0.014 0.001 TYR A 183 ARG 0.008 0.000 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 6) link_NAG-ASN : angle 2.31285 ( 18) link_BETA1-4 : bond 0.00284 ( 1) link_BETA1-4 : angle 1.14937 ( 3) hydrogen bonds : bond 0.05628 ( 301) hydrogen bonds : angle 4.11634 ( 840) metal coordination : bond 0.00318 ( 2) SS BOND : bond 0.00222 ( 7) SS BOND : angle 0.80487 ( 14) covalent geometry : bond 0.00299 ( 6655) covalent geometry : angle 0.49080 ( 9051) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.701 Fit side-chains REVERT: C 420 VAL cc_start: 0.8185 (t) cc_final: 0.7972 (p) REVERT: C 470 VAL cc_start: 0.8729 (t) cc_final: 0.8486 (p) REVERT: C 489 VAL cc_start: 0.8768 (p) cc_final: 0.8517 (t) REVERT: A 129 THR cc_start: 0.8756 (t) cc_final: 0.8456 (p) REVERT: A 166 GLU cc_start: 0.7986 (tp30) cc_final: 0.7676 (mm-30) REVERT: A 171 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: A 184 VAL cc_start: 0.8342 (t) cc_final: 0.8103 (t) REVERT: A 227 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: A 257 SER cc_start: 0.8971 (t) cc_final: 0.8678 (p) REVERT: A 269 ASP cc_start: 0.8407 (t0) cc_final: 0.8160 (m-30) REVERT: A 325 GLN cc_start: 0.8455 (mt0) cc_final: 0.8238 (tt0) REVERT: A 430 GLU cc_start: 0.7928 (mp0) cc_final: 0.7708 (mp0) REVERT: A 435 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 600 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8225 (mtmt) outliers start: 21 outliers final: 12 residues processed: 145 average time/residue: 1.1846 time to fit residues: 180.3270 Evaluate side-chains 145 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102806 restraints weight = 9477.318| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.21 r_work: 0.3120 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6671 Z= 0.103 Angle : 0.487 9.516 9086 Z= 0.253 Chirality : 0.040 0.290 969 Planarity : 0.004 0.050 1164 Dihedral : 5.396 53.559 1005 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.31 % Allowed : 24.42 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.72 (0.30), residues: 785 helix: 1.66 (0.27), residues: 392 sheet: 1.46 (0.65), residues: 43 loop : -1.07 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.007 0.001 PHE C 387 TYR 0.016 0.001 TYR A 50 ARG 0.006 0.000 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 6) link_NAG-ASN : angle 2.02673 ( 18) link_BETA1-4 : bond 0.00293 ( 1) link_BETA1-4 : angle 1.06467 ( 3) hydrogen bonds : bond 0.04445 ( 301) hydrogen bonds : angle 3.99656 ( 840) metal coordination : bond 0.00166 ( 2) SS BOND : bond 0.00278 ( 7) SS BOND : angle 0.82456 ( 14) covalent geometry : bond 0.00222 ( 6655) covalent geometry : angle 0.47807 ( 9051) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8137 (t) cc_final: 0.7932 (p) REVERT: C 470 VAL cc_start: 0.8718 (t) cc_final: 0.8475 (p) REVERT: C 489 VAL cc_start: 0.8738 (p) cc_final: 0.8478 (t) REVERT: A 129 THR cc_start: 0.8660 (t) cc_final: 0.8319 (p) REVERT: A 171 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: A 206 ASP cc_start: 0.8542 (t0) cc_final: 0.8224 (t0) REVERT: A 227 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 257 SER cc_start: 0.8963 (t) cc_final: 0.8671 (p) REVERT: A 401 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7578 (m-70) REVERT: A 430 GLU cc_start: 0.7940 (mp0) cc_final: 0.7702 (mp0) REVERT: A 435 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 600 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8163 (mtmt) outliers start: 16 outliers final: 7 residues processed: 144 average time/residue: 1.2166 time to fit residues: 184.1741 Evaluate side-chains 142 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101874 restraints weight = 9621.496| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.24 r_work: 0.3108 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6671 Z= 0.114 Angle : 0.482 5.271 9086 Z= 0.253 Chirality : 0.041 0.288 969 Planarity : 0.004 0.050 1164 Dihedral : 5.316 52.968 1005 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.60 % Allowed : 25.00 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.77 (0.30), residues: 785 helix: 1.71 (0.27), residues: 392 sheet: 1.48 (0.65), residues: 43 loop : -1.05 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.009 0.001 PHE A 308 TYR 0.013 0.001 TYR A 50 ARG 0.006 0.000 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 6) link_NAG-ASN : angle 2.00370 ( 18) link_BETA1-4 : bond 0.00407 ( 1) link_BETA1-4 : angle 1.15212 ( 3) hydrogen bonds : bond 0.04892 ( 301) hydrogen bonds : angle 3.96617 ( 840) metal coordination : bond 0.00229 ( 2) SS BOND : bond 0.00305 ( 7) SS BOND : angle 0.72966 ( 14) covalent geometry : bond 0.00253 ( 6655) covalent geometry : angle 0.47364 ( 9051) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: C 420 VAL cc_start: 0.8131 (t) cc_final: 0.7910 (p) REVERT: C 470 VAL cc_start: 0.8736 (t) cc_final: 0.8495 (p) REVERT: C 489 VAL cc_start: 0.8752 (p) cc_final: 0.8490 (t) REVERT: A 129 THR cc_start: 0.8704 (t) cc_final: 0.8378 (p) REVERT: A 171 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: A 206 ASP cc_start: 0.8578 (t0) cc_final: 0.8249 (t0) REVERT: A 227 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: A 257 SER cc_start: 0.8984 (t) cc_final: 0.8694 (p) REVERT: A 270 MET cc_start: 0.8259 (tpp) cc_final: 0.7954 (ttp) REVERT: A 401 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7632 (m-70) REVERT: A 430 GLU cc_start: 0.7939 (mp0) cc_final: 0.7700 (mp0) REVERT: A 435 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 600 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8218 (mtmt) outliers start: 18 outliers final: 9 residues processed: 140 average time/residue: 1.1602 time to fit residues: 170.5878 Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101529 restraints weight = 9637.474| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.25 r_work: 0.3081 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6671 Z= 0.129 Angle : 0.514 10.985 9086 Z= 0.265 Chirality : 0.041 0.301 969 Planarity : 0.004 0.052 1164 Dihedral : 5.308 53.246 1005 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 25.72 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.78 (0.30), residues: 785 helix: 1.73 (0.27), residues: 392 sheet: 1.54 (0.66), residues: 43 loop : -1.07 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.005 0.001 HIS A 374 PHE 0.011 0.001 PHE A 308 TYR 0.013 0.001 TYR A 183 ARG 0.009 0.000 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 6) link_NAG-ASN : angle 2.07261 ( 18) link_BETA1-4 : bond 0.00332 ( 1) link_BETA1-4 : angle 1.18782 ( 3) hydrogen bonds : bond 0.05421 ( 301) hydrogen bonds : angle 3.99235 ( 840) metal coordination : bond 0.00286 ( 2) SS BOND : bond 0.00294 ( 7) SS BOND : angle 0.75232 ( 14) covalent geometry : bond 0.00294 ( 6655) covalent geometry : angle 0.50538 ( 9051) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.669 Fit side-chains REVERT: C 470 VAL cc_start: 0.8744 (t) cc_final: 0.8509 (p) REVERT: C 489 VAL cc_start: 0.8760 (p) cc_final: 0.8497 (t) REVERT: A 129 THR cc_start: 0.8749 (t) cc_final: 0.8474 (p) REVERT: A 171 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: A 184 VAL cc_start: 0.8335 (t) cc_final: 0.8019 (t) REVERT: A 206 ASP cc_start: 0.8583 (t0) cc_final: 0.8239 (t0) REVERT: A 227 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 257 SER cc_start: 0.8984 (t) cc_final: 0.8694 (p) REVERT: A 270 MET cc_start: 0.8229 (tpp) cc_final: 0.7979 (ttp) REVERT: A 401 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7657 (m-70) REVERT: A 406 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8134 (mm-30) REVERT: A 430 GLU cc_start: 0.7948 (mp0) cc_final: 0.7700 (mp0) REVERT: A 435 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7553 (mm-30) REVERT: A 600 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8234 (mtmt) outliers start: 17 outliers final: 11 residues processed: 142 average time/residue: 1.3466 time to fit residues: 200.1078 Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099032 restraints weight = 9696.559| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.23 r_work: 0.3039 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6671 Z= 0.198 Angle : 0.556 5.441 9086 Z= 0.290 Chirality : 0.045 0.355 969 Planarity : 0.004 0.052 1164 Dihedral : 5.642 53.690 1005 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 25.58 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.68 (0.30), residues: 785 helix: 1.77 (0.27), residues: 384 sheet: 1.40 (0.66), residues: 44 loop : -1.20 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.007 0.001 HIS A 374 PHE 0.016 0.001 PHE A 308 TYR 0.016 0.002 TYR A 516 ARG 0.009 0.001 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 6) link_NAG-ASN : angle 2.80596 ( 18) link_BETA1-4 : bond 0.00151 ( 1) link_BETA1-4 : angle 1.36477 ( 3) hydrogen bonds : bond 0.06907 ( 301) hydrogen bonds : angle 4.12956 ( 840) metal coordination : bond 0.00542 ( 2) SS BOND : bond 0.00315 ( 7) SS BOND : angle 0.91548 ( 14) covalent geometry : bond 0.00463 ( 6655) covalent geometry : angle 0.54115 ( 9051) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: C 470 VAL cc_start: 0.8755 (t) cc_final: 0.8530 (p) REVERT: C 489 VAL cc_start: 0.8787 (p) cc_final: 0.8522 (t) REVERT: A 95 LEU cc_start: 0.8640 (mt) cc_final: 0.8332 (mp) REVERT: A 129 THR cc_start: 0.8842 (t) cc_final: 0.8603 (p) REVERT: A 171 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: A 227 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: A 257 SER cc_start: 0.8976 (t) cc_final: 0.8685 (p) REVERT: A 269 ASP cc_start: 0.8319 (t0) cc_final: 0.8049 (m-30) REVERT: A 270 MET cc_start: 0.8343 (tpp) cc_final: 0.7914 (ttp) REVERT: A 406 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8106 (mm-30) REVERT: A 435 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 600 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8275 (mtmt) outliers start: 17 outliers final: 10 residues processed: 141 average time/residue: 1.5145 time to fit residues: 224.1217 Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101586 restraints weight = 9840.232| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.27 r_work: 0.3087 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6671 Z= 0.123 Angle : 0.525 11.742 9086 Z= 0.269 Chirality : 0.042 0.308 969 Planarity : 0.004 0.052 1164 Dihedral : 5.521 53.461 1005 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.02 % Allowed : 25.87 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.77 (0.30), residues: 785 helix: 1.71 (0.27), residues: 392 sheet: 1.60 (0.65), residues: 43 loop : -1.07 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.011 0.001 PHE A 308 TYR 0.013 0.001 TYR A 50 ARG 0.008 0.000 ARG C 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 6) link_NAG-ASN : angle 2.54461 ( 18) link_BETA1-4 : bond 0.00425 ( 1) link_BETA1-4 : angle 1.17028 ( 3) hydrogen bonds : bond 0.05172 ( 301) hydrogen bonds : angle 3.98367 ( 840) metal coordination : bond 0.00258 ( 2) SS BOND : bond 0.00291 ( 7) SS BOND : angle 0.69577 ( 14) covalent geometry : bond 0.00275 ( 6655) covalent geometry : angle 0.51252 ( 9051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5319.29 seconds wall clock time: 93 minutes 29.58 seconds (5609.58 seconds total)