Starting phenix.real_space_refine on Thu Jul 2 03:30:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wys_37937/07_2026/8wys_37937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wys_37937/07_2026/8wys_37937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wys_37937/07_2026/8wys_37937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wys_37937/07_2026/8wys_37937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wys_37937/07_2026/8wys_37937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wys_37937/07_2026/8wys_37937.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 46 5.16 5 C 3949 2.51 5 N 1104 2.21 5 O 1239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6340 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "L" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "M" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1669 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain: "J" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 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: 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 Chain: "L" 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 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 1.57, per 1000 atoms: 0.25 Number of scatterers: 6340 At special positions: 0 Unit cell: (64.74, 90.47, 148.57, 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) Ca 2 19.99 S 46 16.00 O 1239 8.00 N 1104 7.00 C 3949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.02 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.04 Simple disulfide: pdb=" SG CYS L 414 " - pdb=" SG CYS M 191 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 575 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS M 147 " - pdb=" SG CYS M 181 " distance=2.03 Simple disulfide: pdb=" SG CYS M 163 " - pdb=" SG CYS M 228 " distance=2.03 Simple disulfide: pdb=" SG CYS M 176 " - pdb=" SG CYS M 238 " distance=2.02 Simple disulfide: pdb=" SG CYS M 208 " - pdb=" SG CYS M 218 " distance=2.03 Simple disulfide: pdb=" SG CYS M 253 " - pdb=" SG CYS M 287 " distance=2.03 Simple disulfide: pdb=" SG CYS M 269 " - pdb=" SG CYS M 335 " distance=2.03 Simple disulfide: pdb=" SG CYS M 282 " - pdb=" SG CYS M 345 " distance=2.03 Simple disulfide: pdb=" SG CYS M 315 " - pdb=" SG CYS M 325 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.02 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 601 " - " ASN A 563 " " NAG B 1 " - " ASN J 48 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 188.1 milliseconds 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1518 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 20 sheets defined 12.2% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.984A pdb=" N LYS A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 421 removed outlier: 3.876A pdb=" N TRP L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY L 421 " --> pdb=" O ASP L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 removed outlier: 3.722A pdb=" N ASN L 465 " --> pdb=" O ARG L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 529 Processing helix chain 'M' and resid 168 through 180 Processing helix chain 'M' and resid 274 through 285 removed outlier: 3.571A pdb=" N LEU M 285 " --> pdb=" O VAL M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 Processing helix chain 'M' and resid 336 through 340 removed outlier: 3.529A pdb=" N GLU M 339 " --> pdb=" O THR M 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 68 Processing helix chain 'J' and resid 129 through 134 removed outlier: 4.293A pdb=" N CYS J 133 " --> pdb=" O THR J 129 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR J 134 " --> pdb=" O PRO J 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 129 through 134' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AA2, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.655A pdb=" N THR A 363 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 413 " --> pdb=" O THR A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 382 through 383 removed outlier: 3.544A pdb=" N THR A 425 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 428 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A 437 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 4.012A pdb=" N THR A 477 " --> pdb=" O ASP A 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 457 removed outlier: 4.012A pdb=" N THR A 477 " --> pdb=" O ASP A 453 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.515A pdb=" N GLN A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 565 through 568 removed outlier: 6.095A pdb=" N SER A 565 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR J 62 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 567 " --> pdb=" O TYR J 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 346 through 347 removed outlier: 3.603A pdb=" N LEU L 365 " --> pdb=" O ALA L 411 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS L 367 " --> pdb=" O GLY L 409 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY L 409 " --> pdb=" O CYS L 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 382 through 383 removed outlier: 3.627A pdb=" N THR L 425 " --> pdb=" O THR L 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS L 426 " --> pdb=" O GLN L 439 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN L 439 " --> pdb=" O CYS L 426 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL L 428 " --> pdb=" O LEU L 437 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU L 437 " --> pdb=" O VAL L 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.641A pdb=" N THR L 477 " --> pdb=" O ASP L 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.641A pdb=" N THR L 477 " --> pdb=" O ASP L 453 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AB4, first strand: chain 'L' and resid 561 through 569 removed outlier: 7.378A pdb=" N LEU L 561 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE J 37 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN L 563 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE J 39 " --> pdb=" O ASN L 563 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER L 565 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL J 41 " --> pdb=" O SER L 565 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL L 567 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA J 15 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP J 9 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE J 5 " --> pdb=" O SER J 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 561 through 569 removed outlier: 7.378A pdb=" N LEU L 561 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE J 37 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN L 563 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE J 39 " --> pdb=" O ASN L 563 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER L 565 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL J 41 " --> pdb=" O SER L 565 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL L 567 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 140 through 141 Processing sheet with id=AB7, first strand: chain 'M' and resid 140 through 141 removed outlier: 5.288A pdb=" N THR M 234 " --> pdb=" O VAL M 151 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP M 233 " --> pdb=" O ARG M 190 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 243 through 248 removed outlier: 4.324A pdb=" N ASP M 243 " --> pdb=" O LEU M 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 243 through 248 removed outlier: 4.324A pdb=" N ASP M 243 " --> pdb=" O LEU M 260 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY M 255 " --> pdb=" O VAL M 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AC2, first strand: chain 'J' and resid 110 through 115 176 hydrogen bonds defined for protein. 462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2074 1.34 - 1.47: 1510 1.47 - 1.59: 2846 1.59 - 1.72: 1 1.72 - 1.85: 54 Bond restraints: 6485 Sorted by residual: bond pdb=" CA ASP M 270 " pdb=" C ASP M 270 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.64e+01 bond pdb=" CA ASN M 272 " pdb=" C ASN M 272 " ideal model delta sigma weight residual 1.531 1.489 0.043 1.08e-02 8.57e+03 1.55e+01 bond pdb=" N ASP M 271 " pdb=" CA ASP M 271 " ideal model delta sigma weight residual 1.457 1.419 0.038 1.30e-02 5.92e+03 8.42e+00 bond pdb=" CB PRO M 200 " pdb=" CG PRO M 200 " ideal model delta sigma weight residual 1.492 1.637 -0.145 5.00e-02 4.00e+02 8.36e+00 bond pdb=" CA ASN M 272 " pdb=" CB ASN M 272 " ideal model delta sigma weight residual 1.532 1.499 0.033 1.36e-02 5.41e+03 5.85e+00 ... (remaining 6480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 8661 2.76 - 5.52: 144 5.52 - 8.28: 29 8.28 - 11.03: 6 11.03 - 13.79: 1 Bond angle restraints: 8841 Sorted by residual: angle pdb=" CA PRO M 200 " pdb=" N PRO M 200 " pdb=" CD PRO M 200 " ideal model delta sigma weight residual 112.00 98.21 13.79 1.40e+00 5.10e-01 9.71e+01 angle pdb=" N ILE L 350 " pdb=" CA ILE L 350 " pdb=" C ILE L 350 " ideal model delta sigma weight residual 108.95 115.45 -6.50 9.80e-01 1.04e+00 4.39e+01 angle pdb=" N PRO M 200 " pdb=" CA PRO M 200 " pdb=" C PRO M 200 " ideal model delta sigma weight residual 111.19 120.55 -9.36 1.57e+00 4.06e-01 3.56e+01 angle pdb=" N GLU M 136 " pdb=" CA GLU M 136 " pdb=" C GLU M 136 " ideal model delta sigma weight residual 110.44 104.38 6.06 1.20e+00 6.94e-01 2.55e+01 angle pdb=" CA PRO J 52 " pdb=" N PRO J 52 " pdb=" CD PRO J 52 " ideal model delta sigma weight residual 112.00 105.25 6.75 1.40e+00 5.10e-01 2.32e+01 ... (remaining 8836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3376 17.89 - 35.78: 469 35.78 - 53.67: 139 53.67 - 71.57: 21 71.57 - 89.46: 10 Dihedral angle restraints: 4015 sinusoidal: 1674 harmonic: 2341 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 426 " pdb=" CB CYS A 426 " ideal model delta sinusoidal sigma weight residual 93.00 178.69 -85.69 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS L 575 " pdb=" SG CYS L 575 " pdb=" SG CYS J 14 " pdb=" CB CYS J 14 " ideal model delta sinusoidal sigma weight residual 93.00 170.49 -77.49 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS M 269 " pdb=" SG CYS M 269 " pdb=" SG CYS M 335 " pdb=" CB CYS M 335 " ideal model delta sinusoidal sigma weight residual 93.00 170.27 -77.27 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 4012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 897 0.089 - 0.178: 107 0.178 - 0.266: 9 0.266 - 0.355: 1 0.355 - 0.444: 1 Chirality restraints: 1015 Sorted by residual: chirality pdb=" CA PRO M 200 " pdb=" N PRO M 200 " pdb=" C PRO M 200 " pdb=" CB PRO M 200 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CA ASN M 272 " pdb=" N ASN M 272 " pdb=" C ASN M 272 " pdb=" CB ASN M 272 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL M 134 " pdb=" CA VAL M 134 " pdb=" CG1 VAL M 134 " pdb=" CG2 VAL M 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1012 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 51 " -0.095 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO J 52 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO J 52 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO J 52 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS M 199 " 0.085 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO M 200 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO M 200 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO M 200 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 134 " 0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO M 135 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO M 135 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 135 " 0.037 5.00e-02 4.00e+02 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 77 2.60 - 3.17: 4863 3.17 - 3.75: 9697 3.75 - 4.32: 13004 4.32 - 4.90: 21575 Nonbonded interactions: 49216 Sorted by model distance: nonbonded pdb=" OE2 GLU M 339 " pdb="CA CA M 401 " model vdw 2.025 3.250 nonbonded pdb=" OD2 ASP M 271 " pdb="CA CA M 402 " model vdw 2.054 3.250 nonbonded pdb=" OD1 ASP M 311 " pdb="CA CA M 402 " model vdw 2.189 3.250 nonbonded pdb=" O VAL J 61 " pdb=" OH TYR J 101 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR L 363 " pdb=" O ILE L 413 " model vdw 2.289 3.040 ... (remaining 49211 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 'A' selection = chain 'L' } 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: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 0.145 6507 Z= 0.262 Angle : 0.921 13.792 8889 Z= 0.502 Chirality : 0.057 0.444 1015 Planarity : 0.009 0.140 1141 Dihedral : 17.488 89.456 2443 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.98 % Allowed : 30.91 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.27), residues: 795 helix: -3.89 (0.27), residues: 90 sheet: -1.26 (0.39), residues: 178 loop : -2.19 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 16 TYR 0.028 0.002 TYR A 500 PHE 0.019 0.002 PHE L 479 TRP 0.045 0.003 TRP A 382 HIS 0.011 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.26 ( 6485) covalent geometry : angle 0.91616 / 0.50 ( 8841) SS BOND : bond 0.00455 / 0.29 ( 18) SS BOND : angle 1.33670 / 1.09 ( 36) hydrogen bonds : bond 0.25364 / 17.45 ( 151) hydrogen bonds : angle 9.68375 / 6.57 ( 462) link_BETA1-4 : bond 0.00685 / 0.36 ( 1) link_BETA1-4 : angle 1.22077 / 0.58 ( 3) link_NAG-ASN : bond 0.00378 / 0.18 ( 3) link_NAG-ASN : angle 2.28505 / 0.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: M 156 GLN cc_start: 0.6898 (pm20) cc_final: 0.6612 (pm20) outliers start: 7 outliers final: 4 residues processed: 121 average time/residue: 0.0857 time to fit residues: 13.7255 Evaluate side-chains 113 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 83 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.0000 chunk 74 optimal weight: 1.9990 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 HIS ** 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 = 0.4228 r_free = 0.4228 target = 0.188018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149759 restraints weight = 9191.001| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.04 r_work: 0.3666 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6507 Z= 0.124 Angle : 0.574 11.949 8889 Z= 0.293 Chirality : 0.045 0.261 1015 Planarity : 0.006 0.079 1141 Dihedral : 5.892 52.743 961 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.59 % Allowed : 26.15 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.28), residues: 795 helix: -2.68 (0.42), residues: 87 sheet: -1.51 (0.36), residues: 190 loop : -1.70 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 16 TYR 0.012 0.001 TYR A 375 PHE 0.012 0.001 PHE L 479 TRP 0.012 0.001 TRP A 418 HIS 0.003 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 6485) covalent geometry : angle 0.57006 / 0.29 ( 8841) SS BOND : bond 0.00240 / 0.16 ( 18) SS BOND : angle 0.71649 / 0.59 ( 36) hydrogen bonds : bond 0.04250 / 2.71 ( 151) hydrogen bonds : angle 6.05770 / 4.14 ( 462) link_BETA1-4 : bond 0.00316 / 0.17 ( 1) link_BETA1-4 : angle 0.91006 / 0.42 ( 3) link_NAG-ASN : bond 0.00242 / 0.12 ( 3) link_NAG-ASN : angle 1.92782 / 0.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.239 Fit side-chains REVERT: A 367 CYS cc_start: 0.3797 (OUTLIER) cc_final: 0.2888 (p) REVERT: A 570 ASP cc_start: 0.7081 (t0) cc_final: 0.6829 (t0) REVERT: L 382 TRP cc_start: 0.5933 (m100) cc_final: 0.5283 (m100) REVERT: L 515 TYR cc_start: 0.8274 (m-80) cc_final: 0.7563 (m-80) outliers start: 40 outliers final: 22 residues processed: 149 average time/residue: 0.0874 time to fit residues: 17.1905 Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 301 TYR Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 63 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN L 400 HIS M 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.185172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146658 restraints weight = 9205.197| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.03 r_work: 0.3629 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6507 Z= 0.153 Angle : 0.579 9.803 8889 Z= 0.297 Chirality : 0.046 0.257 1015 Planarity : 0.005 0.067 1141 Dihedral : 5.583 49.609 958 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.73 % Allowed : 25.45 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.28), residues: 795 helix: -2.25 (0.45), residues: 87 sheet: -1.45 (0.35), residues: 197 loop : -1.63 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.009 0.001 TYR A 562 PHE 0.013 0.001 PHE A 354 TRP 0.013 0.001 TRP A 382 HIS 0.004 0.001 HIS M 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 6485) covalent geometry : angle 0.57591 / 0.30 ( 8841) SS BOND : bond 0.00291 / 0.19 ( 18) SS BOND : angle 0.65119 / 0.47 ( 36) hydrogen bonds : bond 0.03940 / 2.52 ( 151) hydrogen bonds : angle 5.66491 / 3.89 ( 462) link_BETA1-4 : bond 0.00324 / 0.17 ( 1) link_BETA1-4 : angle 0.81109 / 0.36 ( 3) link_NAG-ASN : bond 0.00365 / 0.18 ( 3) link_NAG-ASN : angle 1.96803 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.251 Fit side-chains REVERT: A 367 CYS cc_start: 0.3878 (OUTLIER) cc_final: 0.2914 (p) REVERT: A 382 TRP cc_start: 0.3466 (m100) cc_final: 0.3024 (m100) REVERT: A 414 CYS cc_start: 0.5788 (OUTLIER) cc_final: 0.5379 (t) REVERT: A 570 ASP cc_start: 0.7097 (t0) cc_final: 0.6777 (t0) REVERT: L 382 TRP cc_start: 0.6013 (m100) cc_final: 0.5401 (m100) REVERT: L 490 GLN cc_start: 0.8064 (tp40) cc_final: 0.7838 (tp40) REVERT: L 515 TYR cc_start: 0.8385 (m-80) cc_final: 0.7724 (m-80) outliers start: 41 outliers final: 24 residues processed: 145 average time/residue: 0.0868 time to fit residues: 16.4796 Evaluate side-chains 134 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 0.0040 chunk 60 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 GLN J 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.186873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148616 restraints weight = 9172.550| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.02 r_work: 0.3656 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6507 Z= 0.110 Angle : 0.543 9.354 8889 Z= 0.275 Chirality : 0.045 0.242 1015 Planarity : 0.005 0.066 1141 Dihedral : 5.270 52.066 958 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.76 % Allowed : 26.29 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.29), residues: 795 helix: -1.84 (0.51), residues: 81 sheet: -1.43 (0.35), residues: 197 loop : -1.47 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 256 TYR 0.009 0.001 TYR A 375 PHE 0.012 0.001 PHE L 479 TRP 0.010 0.001 TRP A 382 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 6485) covalent geometry : angle 0.54053 / 0.27 ( 8841) SS BOND : bond 0.00195 / 0.12 ( 18) SS BOND : angle 0.60042 / 0.45 ( 36) hydrogen bonds : bond 0.03521 / 2.24 ( 151) hydrogen bonds : angle 5.20262 / 3.59 ( 462) link_BETA1-4 : bond 0.00281 / 0.15 ( 1) link_BETA1-4 : angle 0.72188 / 0.33 ( 3) link_NAG-ASN : bond 0.00350 / 0.16 ( 3) link_NAG-ASN : angle 1.68836 / 0.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.272 Fit side-chains REVERT: A 367 CYS cc_start: 0.3725 (OUTLIER) cc_final: 0.2748 (p) REVERT: A 382 TRP cc_start: 0.3428 (m100) cc_final: 0.2891 (m100) REVERT: A 414 CYS cc_start: 0.5622 (OUTLIER) cc_final: 0.5276 (t) REVERT: A 570 ASP cc_start: 0.7002 (t0) cc_final: 0.6723 (t0) REVERT: L 382 TRP cc_start: 0.5976 (m100) cc_final: 0.5344 (m100) REVERT: L 490 GLN cc_start: 0.8001 (tp40) cc_final: 0.7264 (mm-40) REVERT: L 515 TYR cc_start: 0.8339 (m-80) cc_final: 0.7736 (m-80) REVERT: M 192 ASN cc_start: 0.4915 (p0) cc_final: 0.4712 (p0) outliers start: 34 outliers final: 20 residues processed: 147 average time/residue: 0.0899 time to fit residues: 17.4326 Evaluate side-chains 133 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 33 optimal weight: 0.0170 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 67 optimal weight: 0.0370 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** A 540 HIS ** 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 = 0.4232 r_free = 0.4232 target = 0.188430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.150122 restraints weight = 9372.365| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.04 r_work: 0.3673 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6507 Z= 0.103 Angle : 0.545 9.225 8889 Z= 0.274 Chirality : 0.044 0.229 1015 Planarity : 0.005 0.063 1141 Dihedral : 5.087 51.364 958 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.90 % Allowed : 26.43 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.29), residues: 795 helix: -1.63 (0.53), residues: 82 sheet: -1.49 (0.34), residues: 207 loop : -1.36 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 314 TYR 0.008 0.001 TYR A 375 PHE 0.011 0.001 PHE L 479 TRP 0.007 0.001 TRP A 382 HIS 0.004 0.001 HIS M 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 ( 6485) covalent geometry : angle 0.54284 / 0.27 ( 8841) SS BOND : bond 0.00165 / 0.10 ( 18) SS BOND : angle 0.62916 / 0.51 ( 36) hydrogen bonds : bond 0.03378 / 2.15 ( 151) hydrogen bonds : angle 5.01171 / 3.46 ( 462) link_BETA1-4 : bond 0.00356 / 0.19 ( 1) link_BETA1-4 : angle 0.77707 / 0.36 ( 3) link_NAG-ASN : bond 0.00299 / 0.14 ( 3) link_NAG-ASN : angle 1.58104 / 0.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.262 Fit side-chains REVERT: A 367 CYS cc_start: 0.3622 (OUTLIER) cc_final: 0.3066 (p) REVERT: A 382 TRP cc_start: 0.3426 (m100) cc_final: 0.2899 (m100) REVERT: A 414 CYS cc_start: 0.5478 (OUTLIER) cc_final: 0.5154 (t) REVERT: A 570 ASP cc_start: 0.6961 (t0) cc_final: 0.6724 (t0) REVERT: L 382 TRP cc_start: 0.5993 (m100) cc_final: 0.5328 (m100) REVERT: L 515 TYR cc_start: 0.8314 (m-80) cc_final: 0.7674 (m-80) REVERT: M 206 MET cc_start: 0.8113 (ptp) cc_final: 0.7585 (pmm) outliers start: 35 outliers final: 22 residues processed: 140 average time/residue: 0.0887 time to fit residues: 16.3057 Evaluate side-chains 129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 61 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** A 540 HIS ** 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 = 0.4212 r_free = 0.4212 target = 0.186337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.147890 restraints weight = 9204.293| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.01 r_work: 0.3651 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6507 Z= 0.123 Angle : 0.560 9.593 8889 Z= 0.281 Chirality : 0.044 0.234 1015 Planarity : 0.005 0.062 1141 Dihedral : 5.068 52.347 958 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.03 % Allowed : 26.71 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.29), residues: 795 helix: -1.44 (0.54), residues: 82 sheet: -1.43 (0.34), residues: 216 loop : -1.27 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 314 TYR 0.009 0.001 TYR A 562 PHE 0.017 0.001 PHE M 295 TRP 0.008 0.001 TRP A 382 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 6485) covalent geometry : angle 0.55758 / 0.28 ( 8841) SS BOND : bond 0.00219 / 0.14 ( 18) SS BOND : angle 0.62479 / 0.48 ( 36) hydrogen bonds : bond 0.03269 / 2.09 ( 151) hydrogen bonds : angle 4.90709 / 3.38 ( 462) link_BETA1-4 : bond 0.00349 / 0.18 ( 1) link_BETA1-4 : angle 0.77895 / 0.36 ( 3) link_NAG-ASN : bond 0.00263 / 0.13 ( 3) link_NAG-ASN : angle 1.74569 / 0.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.245 Fit side-chains REVERT: A 382 TRP cc_start: 0.3514 (m100) cc_final: 0.3062 (m100) REVERT: A 414 CYS cc_start: 0.5453 (OUTLIER) cc_final: 0.5130 (t) REVERT: A 570 ASP cc_start: 0.7110 (t0) cc_final: 0.6879 (t0) REVERT: L 371 ASP cc_start: 0.1249 (OUTLIER) cc_final: 0.0858 (p0) REVERT: L 382 TRP cc_start: 0.6030 (m100) cc_final: 0.5259 (m100) REVERT: L 515 TYR cc_start: 0.8374 (m-80) cc_final: 0.7739 (m-80) REVERT: M 206 MET cc_start: 0.8022 (ptp) cc_final: 0.7537 (pmm) outliers start: 36 outliers final: 23 residues processed: 139 average time/residue: 0.0770 time to fit residues: 14.3000 Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 371 ASP Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.186820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.148497 restraints weight = 9219.135| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.02 r_work: 0.3656 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6507 Z= 0.119 Angle : 0.569 9.678 8889 Z= 0.282 Chirality : 0.044 0.241 1015 Planarity : 0.004 0.061 1141 Dihedral : 4.982 53.581 958 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.62 % Allowed : 26.71 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.29), residues: 795 helix: -1.39 (0.55), residues: 82 sheet: -1.22 (0.34), residues: 221 loop : -1.28 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 314 TYR 0.017 0.001 TYR L 534 PHE 0.011 0.001 PHE A 354 TRP 0.007 0.001 TRP L 528 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 6485) covalent geometry : angle 0.56610 / 0.28 ( 8841) SS BOND : bond 0.00202 / 0.13 ( 18) SS BOND : angle 0.65339 / 0.47 ( 36) hydrogen bonds : bond 0.03244 / 2.09 ( 151) hydrogen bonds : angle 4.84462 / 3.33 ( 462) link_BETA1-4 : bond 0.00334 / 0.18 ( 1) link_BETA1-4 : angle 0.72154 / 0.33 ( 3) link_NAG-ASN : bond 0.00291 / 0.14 ( 3) link_NAG-ASN : angle 1.73592 / 0.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.295 Fit side-chains REVERT: A 382 TRP cc_start: 0.3537 (m100) cc_final: 0.3208 (m100) REVERT: A 414 CYS cc_start: 0.5440 (OUTLIER) cc_final: 0.5107 (t) REVERT: A 570 ASP cc_start: 0.7193 (t0) cc_final: 0.6959 (t0) REVERT: L 382 TRP cc_start: 0.6067 (m100) cc_final: 0.5293 (m100) REVERT: L 515 TYR cc_start: 0.8401 (m-80) cc_final: 0.7975 (m-80) outliers start: 33 outliers final: 24 residues processed: 137 average time/residue: 0.0877 time to fit residues: 16.1067 Evaluate side-chains 131 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 89 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.185757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147214 restraints weight = 9249.021| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.02 r_work: 0.3643 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6507 Z= 0.135 Angle : 0.580 9.876 8889 Z= 0.288 Chirality : 0.045 0.237 1015 Planarity : 0.005 0.060 1141 Dihedral : 5.022 53.879 958 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.76 % Allowed : 27.27 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.30), residues: 795 helix: -1.36 (0.55), residues: 82 sheet: -1.21 (0.36), residues: 206 loop : -1.21 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 314 TYR 0.019 0.001 TYR L 534 PHE 0.016 0.001 PHE M 295 TRP 0.009 0.001 TRP M 167 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 6485) covalent geometry : angle 0.57644 / 0.29 ( 8841) SS BOND : bond 0.00272 / 0.19 ( 18) SS BOND : angle 0.71388 / 0.51 ( 36) hydrogen bonds : bond 0.03306 / 2.13 ( 151) hydrogen bonds : angle 4.82149 / 3.31 ( 462) link_BETA1-4 : bond 0.00459 / 0.24 ( 1) link_BETA1-4 : angle 0.77615 / 0.36 ( 3) link_NAG-ASN : bond 0.00272 / 0.13 ( 3) link_NAG-ASN : angle 1.76207 / 0.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.246 Fit side-chains REVERT: A 382 TRP cc_start: 0.3693 (m100) cc_final: 0.3309 (m100) REVERT: A 414 CYS cc_start: 0.5453 (OUTLIER) cc_final: 0.5104 (t) REVERT: A 570 ASP cc_start: 0.7183 (t0) cc_final: 0.6938 (t0) REVERT: L 382 TRP cc_start: 0.6083 (m100) cc_final: 0.5228 (m100) REVERT: L 515 TYR cc_start: 0.8434 (m-80) cc_final: 0.7825 (m-80) REVERT: M 206 MET cc_start: 0.8060 (pmm) cc_final: 0.7838 (pmm) REVERT: M 277 GLU cc_start: 0.7283 (pm20) cc_final: 0.7046 (pm20) outliers start: 34 outliers final: 26 residues processed: 130 average time/residue: 0.0841 time to fit residues: 14.5883 Evaluate side-chains 131 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 89 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 74 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.0370 chunk 53 optimal weight: 6.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN ** A 540 HIS ** 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 = 0.4219 r_free = 0.4219 target = 0.186841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148886 restraints weight = 9304.106| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.02 r_work: 0.3662 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6507 Z= 0.117 Angle : 0.593 11.010 8889 Z= 0.294 Chirality : 0.044 0.232 1015 Planarity : 0.004 0.061 1141 Dihedral : 4.959 53.326 958 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.34 % Allowed : 27.41 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.30), residues: 795 helix: -1.31 (0.55), residues: 82 sheet: -1.26 (0.36), residues: 201 loop : -1.13 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 314 TYR 0.028 0.001 TYR M 301 PHE 0.011 0.001 PHE A 354 TRP 0.009 0.001 TRP M 202 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 6485) covalent geometry : angle 0.58497 / 0.29 ( 8841) SS BOND : bond 0.00184 / 0.11 ( 18) SS BOND : angle 1.43153 / 1.22 ( 36) hydrogen bonds : bond 0.03226 / 2.07 ( 151) hydrogen bonds : angle 4.74161 / 3.25 ( 462) link_BETA1-4 : bond 0.00399 / 0.21 ( 1) link_BETA1-4 : angle 0.64624 / 0.28 ( 3) link_NAG-ASN : bond 0.00291 / 0.14 ( 3) link_NAG-ASN : angle 1.62813 / 0.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.248 Fit side-chains REVERT: A 382 TRP cc_start: 0.3676 (m100) cc_final: 0.3313 (m100) REVERT: A 414 CYS cc_start: 0.5399 (OUTLIER) cc_final: 0.5060 (t) REVERT: A 570 ASP cc_start: 0.7179 (t0) cc_final: 0.6966 (t0) REVERT: L 382 TRP cc_start: 0.6079 (m100) cc_final: 0.5208 (m100) REVERT: L 515 TYR cc_start: 0.8388 (m-80) cc_final: 0.7954 (m-80) REVERT: M 277 GLU cc_start: 0.7279 (pm20) cc_final: 0.7050 (pm20) outliers start: 31 outliers final: 25 residues processed: 133 average time/residue: 0.0814 time to fit residues: 14.5038 Evaluate side-chains 129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.184068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145775 restraints weight = 9174.454| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.99 r_work: 0.3629 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6507 Z= 0.150 Angle : 0.608 10.276 8889 Z= 0.302 Chirality : 0.045 0.231 1015 Planarity : 0.005 0.060 1141 Dihedral : 5.094 54.375 958 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.92 % Allowed : 28.11 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.30), residues: 795 helix: -1.26 (0.55), residues: 82 sheet: -1.03 (0.37), residues: 196 loop : -1.24 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 314 TYR 0.019 0.001 TYR M 301 PHE 0.015 0.001 PHE M 295 TRP 0.008 0.001 TRP A 382 HIS 0.005 0.001 HIS L 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 6485) covalent geometry : angle 0.60513 / 0.30 ( 8841) SS BOND : bond 0.00270 / 0.17 ( 18) SS BOND : angle 0.81001 / 0.60 ( 36) hydrogen bonds : bond 0.03292 / 2.10 ( 151) hydrogen bonds : angle 4.86193 / 3.33 ( 462) link_BETA1-4 : bond 0.00346 / 0.18 ( 1) link_BETA1-4 : angle 0.70415 / 0.31 ( 3) link_NAG-ASN : bond 0.00252 / 0.12 ( 3) link_NAG-ASN : angle 1.74729 / 0.70 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.244 Fit side-chains REVERT: A 414 CYS cc_start: 0.5458 (OUTLIER) cc_final: 0.5078 (t) REVERT: A 570 ASP cc_start: 0.7261 (t0) cc_final: 0.6997 (t0) REVERT: L 382 TRP cc_start: 0.6127 (m100) cc_final: 0.5257 (m100) REVERT: L 515 TYR cc_start: 0.8450 (m-80) cc_final: 0.7832 (m-80) REVERT: M 277 GLU cc_start: 0.7254 (pm20) cc_final: 0.6623 (pm20) outliers start: 28 outliers final: 24 residues processed: 130 average time/residue: 0.0849 time to fit residues: 14.7548 Evaluate side-chains 131 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 465 ASN J 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.181246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143401 restraints weight = 9193.848| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.93 r_work: 0.3590 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6507 Z= 0.181 Angle : 0.634 11.871 8889 Z= 0.317 Chirality : 0.046 0.229 1015 Planarity : 0.005 0.059 1141 Dihedral : 5.370 56.829 958 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.92 % Allowed : 28.25 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.30), residues: 795 helix: -1.23 (0.55), residues: 82 sheet: -1.35 (0.36), residues: 209 loop : -1.22 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 245 TYR 0.023 0.002 TYR L 534 PHE 0.016 0.001 PHE A 354 TRP 0.019 0.001 TRP A 382 HIS 0.003 0.001 HIS J 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 6485) covalent geometry : angle 0.63079 / 0.32 ( 8841) SS BOND : bond 0.00365 / 0.23 ( 18) SS BOND : angle 0.92674 / 0.69 ( 36) hydrogen bonds : bond 0.03413 / 2.19 ( 151) hydrogen bonds : angle 5.13111 / 3.51 ( 462) link_BETA1-4 : bond 0.00347 / 0.18 ( 1) link_BETA1-4 : angle 0.65269 / 0.29 ( 3) link_NAG-ASN : bond 0.00267 / 0.13 ( 3) link_NAG-ASN : angle 1.77587 / 0.72 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.17 seconds wall clock time: 32 minutes 21.27 seconds (1941.27 seconds total)