Starting phenix.real_space_refine on Sat May 10 13:34:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wys_37937/05_2025/8wys_37937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wys_37937/05_2025/8wys_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wys_37937/05_2025/8wys_37937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wys_37937/05_2025/8wys_37937.map" model { file = "/net/cci-nas-00/data/ceres_data/8wys_37937/05_2025/8wys_37937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wys_37937/05_2025/8wys_37937.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.02, per 1000 atoms: 0.79 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: 1.68 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.93 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: 1.83 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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 2.510 nonbonded pdb=" OD2 ASP M 271 " pdb="CA CA M 402 " model vdw 2.054 2.510 nonbonded pdb=" OD1 ASP M 311 " pdb="CA CA M 402 " model vdw 2.189 2.510 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: 3.730 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.310 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 (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: -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 TRP 0.045 0.003 TRP A 382 HIS 0.011 0.001 HIS A 450 PHE 0.019 0.002 PHE L 479 TYR 0.028 0.002 TYR A 500 ARG 0.019 0.001 ARG J 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 3) link_NAG-ASN : angle 2.28505 ( 9) link_BETA1-4 : bond 0.00685 ( 1) link_BETA1-4 : angle 1.22077 ( 3) hydrogen bonds : bond 0.25364 ( 151) hydrogen bonds : angle 9.68375 ( 462) SS BOND : bond 0.00455 ( 18) SS BOND : angle 1.33670 ( 36) covalent geometry : bond 0.00546 ( 6485) covalent geometry : angle 0.91616 ( 8841) *********************** 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 : 0.702 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: 0.1962 time to fit residues: 30.8314 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 : 0.686 ------------------------------------------------------------------------------- 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 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.185963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147709 restraints weight = 9107.772| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.01 r_work: 0.3642 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6507 Z= 0.148 Angle : 0.594 11.674 8889 Z= 0.304 Chirality : 0.045 0.270 1015 Planarity : 0.006 0.080 1141 Dihedral : 6.045 52.563 961 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.17 % Allowed : 26.43 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.28), residues: 795 helix: -2.71 (0.41), residues: 87 sheet: -1.52 (0.36), residues: 190 loop : -1.70 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 382 HIS 0.003 0.001 HIS A 450 PHE 0.013 0.001 PHE A 354 TYR 0.012 0.001 TYR A 375 ARG 0.006 0.000 ARG J 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 3) link_NAG-ASN : angle 2.05231 ( 9) link_BETA1-4 : bond 0.00165 ( 1) link_BETA1-4 : angle 0.82054 ( 3) hydrogen bonds : bond 0.04498 ( 151) hydrogen bonds : angle 6.17732 ( 462) SS BOND : bond 0.00304 ( 18) SS BOND : angle 0.74610 ( 36) covalent geometry : bond 0.00348 ( 6485) covalent geometry : angle 0.58971 ( 8841) *********************** 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 156 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.617 Fit side-chains REVERT: A 367 CYS cc_start: 0.3820 (OUTLIER) cc_final: 0.2933 (p) REVERT: A 570 ASP cc_start: 0.7118 (t0) cc_final: 0.6884 (t0) REVERT: L 382 TRP cc_start: 0.5916 (m100) cc_final: 0.5144 (m100) REVERT: L 515 TYR cc_start: 0.8326 (m-80) cc_final: 0.7595 (m-80) outliers start: 37 outliers final: 19 residues processed: 146 average time/residue: 0.1869 time to fit residues: 35.6911 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN L 400 HIS J 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.183178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144802 restraints weight = 9264.709| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.01 r_work: 0.3609 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6507 Z= 0.162 Angle : 0.589 9.643 8889 Z= 0.301 Chirality : 0.046 0.264 1015 Planarity : 0.005 0.066 1141 Dihedral : 5.722 53.663 958 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.73 % Allowed : 24.76 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.28), residues: 795 helix: -2.15 (0.48), residues: 82 sheet: -1.39 (0.35), residues: 202 loop : -1.66 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.003 0.001 HIS A 518 PHE 0.014 0.001 PHE A 354 TYR 0.012 0.001 TYR A 562 ARG 0.003 0.000 ARG M 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 3) link_NAG-ASN : angle 2.01351 ( 9) link_BETA1-4 : bond 0.00324 ( 1) link_BETA1-4 : angle 0.76874 ( 3) hydrogen bonds : bond 0.03941 ( 151) hydrogen bonds : angle 5.65522 ( 462) SS BOND : bond 0.00320 ( 18) SS BOND : angle 0.69165 ( 36) covalent geometry : bond 0.00377 ( 6485) covalent geometry : angle 0.58493 ( 8841) *********************** 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 156 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.656 Fit side-chains REVERT: A 367 CYS cc_start: 0.4224 (OUTLIER) cc_final: 0.3403 (p) REVERT: A 382 TRP cc_start: 0.3524 (m100) cc_final: 0.2996 (m100) REVERT: A 414 CYS cc_start: 0.5785 (OUTLIER) cc_final: 0.5360 (t) REVERT: A 570 ASP cc_start: 0.7140 (t0) cc_final: 0.6827 (t0) REVERT: L 382 TRP cc_start: 0.6000 (m100) cc_final: 0.5346 (m100) REVERT: L 490 GLN cc_start: 0.8043 (tp40) cc_final: 0.7820 (tp40) REVERT: L 515 TYR cc_start: 0.8413 (m-80) cc_final: 0.7829 (m-80) outliers start: 41 outliers final: 24 residues processed: 148 average time/residue: 0.2090 time to fit residues: 40.1139 Evaluate side-chains 136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 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 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 22 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.0010 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142349 restraints weight = 9317.347| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.02 r_work: 0.3579 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6507 Z= 0.186 Angle : 0.603 10.561 8889 Z= 0.306 Chirality : 0.046 0.257 1015 Planarity : 0.005 0.061 1141 Dihedral : 5.740 57.820 958 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.59 % Allowed : 26.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.29), residues: 795 helix: -1.71 (0.53), residues: 82 sheet: -1.50 (0.34), residues: 210 loop : -1.54 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.005 0.001 HIS A 450 PHE 0.015 0.002 PHE A 354 TYR 0.014 0.001 TYR A 562 ARG 0.003 0.000 ARG M 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 3) link_NAG-ASN : angle 1.96410 ( 9) link_BETA1-4 : bond 0.00220 ( 1) link_BETA1-4 : angle 0.62917 ( 3) hydrogen bonds : bond 0.03736 ( 151) hydrogen bonds : angle 5.54671 ( 462) SS BOND : bond 0.00427 ( 18) SS BOND : angle 0.78510 ( 36) covalent geometry : bond 0.00435 ( 6485) covalent geometry : angle 0.59962 ( 8841) *********************** 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 164 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.688 Fit side-chains REVERT: A 367 CYS cc_start: 0.4383 (OUTLIER) cc_final: 0.3742 (p) REVERT: A 414 CYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5339 (t) REVERT: A 570 ASP cc_start: 0.7204 (t0) cc_final: 0.6864 (t0) REVERT: L 382 TRP cc_start: 0.6078 (m100) cc_final: 0.5382 (m100) REVERT: L 515 TYR cc_start: 0.8461 (m-80) cc_final: 0.7820 (m-80) REVERT: L 534 TYR cc_start: 0.8345 (m-80) cc_final: 0.8100 (m-80) REVERT: M 192 ASN cc_start: 0.4997 (p0) cc_final: 0.4780 (p0) outliers start: 40 outliers final: 26 residues processed: 157 average time/residue: 0.1920 time to fit residues: 38.9432 Evaluate side-chains 142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 386 ASN 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 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 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 22 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR 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 12 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** J 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.182399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.144074 restraints weight = 9134.819| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.99 r_work: 0.3600 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6507 Z= 0.149 Angle : 0.599 9.838 8889 Z= 0.301 Chirality : 0.046 0.248 1015 Planarity : 0.005 0.060 1141 Dihedral : 5.575 58.825 958 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.17 % Allowed : 29.23 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.29), residues: 795 helix: -1.51 (0.55), residues: 82 sheet: -1.31 (0.35), residues: 200 loop : -1.55 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 382 HIS 0.004 0.001 HIS M 155 PHE 0.013 0.001 PHE A 354 TYR 0.011 0.001 TYR A 562 ARG 0.007 0.000 ARG M 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 3) link_NAG-ASN : angle 1.86531 ( 9) link_BETA1-4 : bond 0.00250 ( 1) link_BETA1-4 : angle 0.57429 ( 3) hydrogen bonds : bond 0.03529 ( 151) hydrogen bonds : angle 5.33424 ( 462) SS BOND : bond 0.00315 ( 18) SS BOND : angle 1.45897 ( 36) covalent geometry : bond 0.00352 ( 6485) covalent geometry : angle 0.59016 ( 8841) *********************** 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 158 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 367 CYS cc_start: 0.4145 (OUTLIER) cc_final: 0.3497 (p) REVERT: A 414 CYS cc_start: 0.5655 (OUTLIER) cc_final: 0.5254 (t) REVERT: A 570 ASP cc_start: 0.7100 (t0) cc_final: 0.6802 (t0) REVERT: L 382 TRP cc_start: 0.6069 (m100) cc_final: 0.5271 (m100) REVERT: L 490 GLN cc_start: 0.8053 (tp40) cc_final: 0.7848 (tp40) REVERT: L 515 TYR cc_start: 0.8457 (m-80) cc_final: 0.7843 (m-80) REVERT: L 534 TYR cc_start: 0.8315 (m-80) cc_final: 0.8080 (m-80) outliers start: 37 outliers final: 27 residues processed: 152 average time/residue: 0.1936 time to fit residues: 38.2813 Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 386 ASN 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 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 153 VAL 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 22 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 76 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.178281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140060 restraints weight = 9108.608| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.91 r_work: 0.3558 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6507 Z= 0.231 Angle : 0.655 9.694 8889 Z= 0.333 Chirality : 0.048 0.250 1015 Planarity : 0.005 0.058 1141 Dihedral : 5.940 61.982 958 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.57 % Allowed : 27.69 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.29), residues: 795 helix: -1.61 (0.52), residues: 89 sheet: -1.37 (0.35), residues: 199 loop : -1.63 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.004 0.001 HIS J 63 PHE 0.017 0.002 PHE A 354 TYR 0.014 0.001 TYR A 562 ARG 0.005 0.000 ARG M 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 3) link_NAG-ASN : angle 2.07903 ( 9) link_BETA1-4 : bond 0.00317 ( 1) link_BETA1-4 : angle 0.60061 ( 3) hydrogen bonds : bond 0.03702 ( 151) hydrogen bonds : angle 5.57515 ( 462) SS BOND : bond 0.00452 ( 18) SS BOND : angle 1.10748 ( 36) covalent geometry : bond 0.00544 ( 6485) covalent geometry : angle 0.64965 ( 8841) *********************** 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 168 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.796 Fit side-chains REVERT: A 367 CYS cc_start: 0.4499 (OUTLIER) cc_final: 0.3994 (p) REVERT: A 414 CYS cc_start: 0.5793 (OUTLIER) cc_final: 0.5234 (t) REVERT: A 453 ASP cc_start: 0.6274 (OUTLIER) cc_final: 0.6048 (t70) REVERT: A 467 ARG cc_start: 0.8162 (mmm160) cc_final: 0.7900 (mmt180) REVERT: A 518 HIS cc_start: 0.7611 (m-70) cc_final: 0.7361 (m90) REVERT: A 570 ASP cc_start: 0.7367 (t0) cc_final: 0.7044 (t0) REVERT: L 382 TRP cc_start: 0.6046 (m100) cc_final: 0.5222 (m100) REVERT: M 157 ASN cc_start: 0.8577 (t0) cc_final: 0.8315 (t0) REVERT: J 9 ASP cc_start: 0.8199 (t0) cc_final: 0.7986 (t0) REVERT: J 71 CYS cc_start: 0.6072 (OUTLIER) cc_final: 0.5853 (m) outliers start: 47 outliers final: 29 residues processed: 157 average time/residue: 0.1918 time to fit residues: 39.4797 Evaluate side-chains 147 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 386 ASN Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 453 ASP 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 417 ASP 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 153 VAL Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 339 GLU 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 22 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 76 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 52 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 62 optimal weight: 0.0000 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN J 10 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.181201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143471 restraints weight = 8988.998| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.87 r_work: 0.3597 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6507 Z= 0.125 Angle : 0.593 9.244 8889 Z= 0.298 Chirality : 0.046 0.244 1015 Planarity : 0.004 0.059 1141 Dihedral : 5.549 60.532 958 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.73 % Allowed : 28.53 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.29), residues: 795 helix: -1.44 (0.55), residues: 82 sheet: -1.25 (0.35), residues: 201 loop : -1.50 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 382 HIS 0.003 0.001 HIS A 518 PHE 0.013 0.001 PHE A 354 TYR 0.010 0.001 TYR A 375 ARG 0.005 0.000 ARG M 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 3) link_NAG-ASN : angle 1.76915 ( 9) link_BETA1-4 : bond 0.00387 ( 1) link_BETA1-4 : angle 0.53202 ( 3) hydrogen bonds : bond 0.03506 ( 151) hydrogen bonds : angle 5.24177 ( 462) SS BOND : bond 0.00220 ( 18) SS BOND : angle 0.91171 ( 36) covalent geometry : bond 0.00302 ( 6485) covalent geometry : angle 0.58864 ( 8841) *********************** 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 164 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.761 Fit side-chains REVERT: A 367 CYS cc_start: 0.4058 (OUTLIER) cc_final: 0.3425 (p) REVERT: A 414 CYS cc_start: 0.5654 (OUTLIER) cc_final: 0.5246 (t) REVERT: A 453 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5856 (t70) REVERT: A 467 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7892 (mmt180) REVERT: A 570 ASP cc_start: 0.7145 (t0) cc_final: 0.6809 (t0) REVERT: L 382 TRP cc_start: 0.5982 (m100) cc_final: 0.5116 (m100) REVERT: L 490 GLN cc_start: 0.8021 (tp40) cc_final: 0.7813 (tp40) REVERT: L 534 TYR cc_start: 0.8352 (m-80) cc_final: 0.8118 (m-80) REVERT: M 170 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7145 (mtm180) REVERT: M 227 THR cc_start: 0.8357 (m) cc_final: 0.8152 (m) REVERT: M 277 GLU cc_start: 0.7278 (pm20) cc_final: 0.6515 (pm20) REVERT: J 9 ASP cc_start: 0.8197 (t0) cc_final: 0.7978 (t0) outliers start: 41 outliers final: 24 residues processed: 155 average time/residue: 0.2025 time to fit residues: 40.8318 Evaluate side-chains 141 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 453 ASP 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 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 268 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 M residue 344 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 76 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 545 ASN ** J 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.178614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140093 restraints weight = 9109.915| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.93 r_work: 0.3557 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6507 Z= 0.224 Angle : 0.666 10.721 8889 Z= 0.332 Chirality : 0.048 0.234 1015 Planarity : 0.005 0.058 1141 Dihedral : 5.886 62.861 958 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.73 % Allowed : 28.39 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.29), residues: 795 helix: -1.54 (0.54), residues: 82 sheet: -1.34 (0.35), residues: 199 loop : -1.57 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 167 HIS 0.004 0.001 HIS J 63 PHE 0.017 0.002 PHE A 354 TYR 0.018 0.002 TYR J 62 ARG 0.004 0.000 ARG M 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 3) link_NAG-ASN : angle 1.88591 ( 9) link_BETA1-4 : bond 0.00260 ( 1) link_BETA1-4 : angle 0.53481 ( 3) hydrogen bonds : bond 0.03582 ( 151) hydrogen bonds : angle 5.51066 ( 462) SS BOND : bond 0.00497 ( 18) SS BOND : angle 1.07148 ( 36) covalent geometry : bond 0.00533 ( 6485) covalent geometry : angle 0.66122 ( 8841) *********************** 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 156 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.735 Fit side-chains REVERT: A 367 CYS cc_start: 0.4437 (OUTLIER) cc_final: 0.3952 (p) REVERT: A 414 CYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5260 (t) REVERT: A 453 ASP cc_start: 0.6261 (OUTLIER) cc_final: 0.6043 (t70) REVERT: A 467 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7904 (mmt180) REVERT: A 475 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 518 HIS cc_start: 0.7589 (m-70) cc_final: 0.7312 (m90) REVERT: A 570 ASP cc_start: 0.7271 (t0) cc_final: 0.7035 (t0) REVERT: L 382 TRP cc_start: 0.6098 (m100) cc_final: 0.5161 (m100) REVERT: L 515 TYR cc_start: 0.8543 (m-80) cc_final: 0.8225 (m-80) REVERT: M 157 ASN cc_start: 0.8511 (t0) cc_final: 0.8276 (t0) REVERT: M 170 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7227 (mtm180) REVERT: M 277 GLU cc_start: 0.7261 (pm20) cc_final: 0.6636 (pm20) REVERT: M 340 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7914 (t70) outliers start: 41 outliers final: 27 residues processed: 146 average time/residue: 0.1884 time to fit residues: 36.2583 Evaluate side-chains 142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 386 ASN Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 495 LEU 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 496 SER Chi-restraints excluded: chain L residue 498 GLU 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 264 VAL Chi-restraints excluded: chain M residue 268 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 53 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 116 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 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 465 ASN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.178389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140509 restraints weight = 9114.983| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.86 r_work: 0.3558 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6507 Z= 0.177 Angle : 0.639 10.386 8889 Z= 0.320 Chirality : 0.047 0.209 1015 Planarity : 0.005 0.059 1141 Dihedral : 5.774 62.439 958 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 5.03 % Allowed : 29.23 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.29), residues: 795 helix: -1.53 (0.54), residues: 82 sheet: -1.24 (0.38), residues: 185 loop : -1.45 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 167 HIS 0.003 0.001 HIS J 63 PHE 0.015 0.002 PHE A 354 TYR 0.015 0.001 TYR J 62 ARG 0.004 0.000 ARG M 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 3) link_NAG-ASN : angle 1.58727 ( 9) link_BETA1-4 : bond 0.00333 ( 1) link_BETA1-4 : angle 0.46595 ( 3) hydrogen bonds : bond 0.03535 ( 151) hydrogen bonds : angle 5.41097 ( 462) SS BOND : bond 0.00376 ( 18) SS BOND : angle 0.96270 ( 36) covalent geometry : bond 0.00422 ( 6485) covalent geometry : angle 0.63555 ( 8841) *********************** 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 147 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.747 Fit side-chains REVERT: A 367 CYS cc_start: 0.4291 (OUTLIER) cc_final: 0.3722 (p) REVERT: A 414 CYS cc_start: 0.5682 (OUTLIER) cc_final: 0.5277 (t) REVERT: A 453 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5896 (t70) REVERT: A 467 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7930 (mmt180) REVERT: A 570 ASP cc_start: 0.7011 (t0) cc_final: 0.6699 (t0) REVERT: L 382 TRP cc_start: 0.6112 (m100) cc_final: 0.5178 (m100) REVERT: L 515 TYR cc_start: 0.8510 (m-80) cc_final: 0.8156 (m-80) REVERT: M 157 ASN cc_start: 0.8572 (t0) cc_final: 0.8324 (t0) REVERT: M 277 GLU cc_start: 0.7335 (pm20) cc_final: 0.6557 (pm20) outliers start: 36 outliers final: 28 residues processed: 139 average time/residue: 0.1911 time to fit residues: 35.1194 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 : 0.749 ------------------------------------------------------------------------------- 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 453 ASP Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 495 LEU 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 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 153 VAL Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 339 GLU 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 53 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.178160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140350 restraints weight = 9137.534| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.85 r_work: 0.3556 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6507 Z= 0.180 Angle : 0.648 10.721 8889 Z= 0.326 Chirality : 0.047 0.215 1015 Planarity : 0.005 0.059 1141 Dihedral : 5.818 63.207 958 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 5.45 % Allowed : 28.25 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.30), residues: 795 helix: -1.53 (0.53), residues: 82 sheet: -1.17 (0.38), residues: 185 loop : -1.44 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 382 HIS 0.003 0.001 HIS J 63 PHE 0.015 0.002 PHE A 354 TYR 0.022 0.002 TYR L 534 ARG 0.004 0.000 ARG M 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 3) link_NAG-ASN : angle 1.63516 ( 9) link_BETA1-4 : bond 0.00280 ( 1) link_BETA1-4 : angle 0.48848 ( 3) hydrogen bonds : bond 0.03532 ( 151) hydrogen bonds : angle 5.38258 ( 462) SS BOND : bond 0.00388 ( 18) SS BOND : angle 0.93285 ( 36) covalent geometry : bond 0.00432 ( 6485) covalent geometry : angle 0.64474 ( 8841) ********************** 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 148 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.753 Fit side-chains REVERT: A 367 CYS cc_start: 0.4544 (OUTLIER) cc_final: 0.4158 (p) REVERT: A 414 CYS cc_start: 0.5681 (OUTLIER) cc_final: 0.5268 (t) REVERT: A 453 ASP cc_start: 0.6117 (OUTLIER) cc_final: 0.5870 (t70) REVERT: A 467 ARG cc_start: 0.8173 (mmm160) cc_final: 0.7956 (mmt180) REVERT: A 570 ASP cc_start: 0.7056 (t0) cc_final: 0.6781 (t0) REVERT: L 382 TRP cc_start: 0.6107 (m100) cc_final: 0.5171 (m100) REVERT: L 515 TYR cc_start: 0.8517 (m-80) cc_final: 0.8159 (m-80) REVERT: M 156 GLN cc_start: 0.7308 (pm20) cc_final: 0.6939 (pm20) REVERT: M 157 ASN cc_start: 0.8578 (t0) cc_final: 0.8330 (t0) REVERT: M 277 GLU cc_start: 0.7350 (pm20) cc_final: 0.6554 (pm20) outliers start: 39 outliers final: 30 residues processed: 140 average time/residue: 0.1890 time to fit residues: 34.9505 Evaluate side-chains 140 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 453 ASP Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 495 LEU 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 417 ASP Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 498 GLU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 142 ASP Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 268 VAL 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 53 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.0030 chunk 34 optimal weight: 0.0040 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143577 restraints weight = 9238.659| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.90 r_work: 0.3598 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6507 Z= 0.126 Angle : 0.611 11.561 8889 Z= 0.304 Chirality : 0.045 0.207 1015 Planarity : 0.005 0.061 1141 Dihedral : 4.826 25.754 955 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.48 % Allowed : 29.09 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.91 (0.30), residues: 795 helix: -1.49 (0.54), residues: 82 sheet: -1.08 (0.38), residues: 186 loop : -1.33 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP M 167 HIS 0.003 0.001 HIS L 540 PHE 0.013 0.001 PHE L 479 TYR 0.015 0.001 TYR A 375 ARG 0.006 0.000 ARG M 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 3) link_NAG-ASN : angle 1.45648 ( 9) link_BETA1-4 : bond 0.00480 ( 1) link_BETA1-4 : angle 0.59020 ( 3) hydrogen bonds : bond 0.03376 ( 151) hydrogen bonds : angle 5.11712 ( 462) SS BOND : bond 0.00242 ( 18) SS BOND : angle 0.90382 ( 36) covalent geometry : bond 0.00305 ( 6485) covalent geometry : angle 0.60767 ( 8841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3521.66 seconds wall clock time: 61 minutes 46.56 seconds (3706.56 seconds total)