Starting phenix.real_space_refine on Fri Aug 22 17:14:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wys_37937/08_2025/8wys_37937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wys_37937/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wys_37937/08_2025/8wys_37937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wys_37937/08_2025/8wys_37937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wys_37937/08_2025/8wys_37937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wys_37937/08_2025/8wys_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-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.28 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: 0.44 Conformation dependent library (CDL) restraints added in 338.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.26 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: 1.03 Time building geometry restraints manager: 0.63 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: 5.710 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.970 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00546 ( 6485) covalent geometry : angle 0.91616 ( 8841) SS BOND : bond 0.00455 ( 18) SS BOND : angle 1.33670 ( 36) hydrogen bonds : bond 0.25364 ( 151) hydrogen bonds : angle 9.68375 ( 462) link_BETA1-4 : bond 0.00685 ( 1) link_BETA1-4 : angle 1.22077 ( 3) link_NAG-ASN : bond 0.00378 ( 3) link_NAG-ASN : angle 2.28505 ( 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 : 0.245 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: 0.0932 time to fit residues: 14.7344 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 : 0.248 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.188134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149858 restraints weight = 9237.508| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.06 r_work: 0.3665 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1165 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= 0.125 Angle : 0.578 11.387 8889 Z= 0.297 Chirality : 0.045 0.262 1015 Planarity : 0.006 0.080 1141 Dihedral : 5.952 52.936 961 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % 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 aren not related in a simple way. whole: -2.61 (0.28), residues: 795 helix: -2.67 (0.42), residues: 87 sheet: -1.49 (0.36), residues: 190 loop : -1.70 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 16 TYR 0.013 0.001 TYR A 375 PHE 0.011 0.001 PHE L 479 TRP 0.013 0.001 TRP A 418 HIS 0.003 0.001 HIS M 337 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6485) covalent geometry : angle 0.57437 ( 8841) SS BOND : bond 0.00248 ( 18) SS BOND : angle 0.72145 ( 36) hydrogen bonds : bond 0.04485 ( 151) hydrogen bonds : angle 6.10106 ( 462) link_BETA1-4 : bond 0.00268 ( 1) link_BETA1-4 : angle 0.87746 ( 3) link_NAG-ASN : bond 0.00266 ( 3) link_NAG-ASN : angle 1.94724 ( 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 160 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.256 Fit side-chains REVERT: A 367 CYS cc_start: 0.3817 (OUTLIER) cc_final: 0.2919 (p) REVERT: A 570 ASP cc_start: 0.7045 (t0) cc_final: 0.6822 (t0) REVERT: L 515 TYR cc_start: 0.8278 (m-80) cc_final: 0.7543 (m-80) outliers start: 40 outliers final: 22 residues processed: 148 average time/residue: 0.0881 time to fit residues: 17.0676 Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** J 63 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 = 0.4093 r_free = 0.4093 target = 0.175765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137520 restraints weight = 9012.891| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.87 r_work: 0.3514 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 6507 Z= 0.324 Angle : 0.734 10.417 8889 Z= 0.379 Chirality : 0.050 0.292 1015 Planarity : 0.006 0.065 1141 Dihedral : 6.430 57.556 958 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 7.13 % Allowed : 24.76 % 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 aren not related in a simple way. whole: -2.54 (0.28), residues: 795 helix: -2.21 (0.48), residues: 82 sheet: -1.37 (0.35), residues: 200 loop : -1.78 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 16 TYR 0.021 0.002 TYR A 562 PHE 0.022 0.002 PHE A 354 TRP 0.014 0.002 TRP A 382 HIS 0.007 0.001 HIS M 155 Details of bonding type rmsd covalent geometry : bond 0.00749 ( 6485) covalent geometry : angle 0.72852 ( 8841) SS BOND : bond 0.00805 ( 18) SS BOND : angle 0.97145 ( 36) hydrogen bonds : bond 0.04445 ( 151) hydrogen bonds : angle 6.21030 ( 462) link_BETA1-4 : bond 0.00181 ( 1) link_BETA1-4 : angle 0.69631 ( 3) link_NAG-ASN : bond 0.00465 ( 3) link_NAG-ASN : angle 2.57442 ( 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 172 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 CYS cc_start: 0.4605 (OUTLIER) cc_final: 0.3979 (p) REVERT: A 382 TRP cc_start: 0.3719 (m100) cc_final: 0.3172 (m100) REVERT: A 414 CYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5355 (t) REVERT: A 475 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 518 HIS cc_start: 0.7785 (m-70) cc_final: 0.7563 (m-70) REVERT: A 570 ASP cc_start: 0.7386 (t0) cc_final: 0.6976 (t0) REVERT: L 382 TRP cc_start: 0.6051 (m100) cc_final: 0.5211 (m100) REVERT: L 490 GLN cc_start: 0.8085 (tp40) cc_final: 0.7779 (tp40) REVERT: M 157 ASN cc_start: 0.8552 (t0) cc_final: 0.8232 (t0) REVERT: J 11 LYS cc_start: 0.7851 (mmtm) cc_final: 0.7591 (mmtm) outliers start: 51 outliers final: 26 residues processed: 159 average time/residue: 0.0929 time to fit residues: 19.0149 Evaluate side-chains 148 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE 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 475 LEU Chi-restraints excluded: chain A residue 501 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 417 ASP Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 238 CYS Chi-restraints excluded: chain M residue 264 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 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 91 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4128 r_free = 0.4128 target = 0.179014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141275 restraints weight = 8979.141| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.87 r_work: 0.3562 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2087 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= 0.157 Angle : 0.601 8.968 8889 Z= 0.306 Chirality : 0.046 0.269 1015 Planarity : 0.005 0.066 1141 Dihedral : 5.944 59.469 958 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.01 % Allowed : 26.71 % Favored : 67.27 % 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 aren not related in a simple way. whole: -2.38 (0.28), residues: 795 helix: -1.87 (0.52), residues: 82 sheet: -1.38 (0.35), residues: 199 loop : -1.66 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 256 TYR 0.012 0.001 TYR J 62 PHE 0.014 0.001 PHE A 354 TRP 0.009 0.001 TRP L 528 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6485) covalent geometry : angle 0.59698 ( 8841) SS BOND : bond 0.00341 ( 18) SS BOND : angle 0.81795 ( 36) hydrogen bonds : bond 0.03800 ( 151) hydrogen bonds : angle 5.68668 ( 462) link_BETA1-4 : bond 0.00314 ( 1) link_BETA1-4 : angle 0.53722 ( 3) link_NAG-ASN : bond 0.00337 ( 3) link_NAG-ASN : angle 2.04367 ( 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 166 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.225 Fit side-chains REVERT: A 367 CYS cc_start: 0.4244 (OUTLIER) cc_final: 0.3681 (p) REVERT: A 414 CYS cc_start: 0.5655 (OUTLIER) cc_final: 0.5256 (t) REVERT: A 453 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5844 (t70) REVERT: A 570 ASP cc_start: 0.7159 (t0) cc_final: 0.6805 (t0) REVERT: L 382 TRP cc_start: 0.6040 (m100) cc_final: 0.5259 (m100) REVERT: L 534 TYR cc_start: 0.8356 (m-80) cc_final: 0.8153 (m-80) REVERT: M 170 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7078 (mtm180) REVERT: M 192 ASN cc_start: 0.5010 (p0) cc_final: 0.4790 (p0) REVERT: J 11 LYS cc_start: 0.7742 (mmtm) cc_final: 0.7404 (mmtm) outliers start: 43 outliers final: 26 residues processed: 156 average time/residue: 0.0839 time to fit residues: 17.0130 Evaluate side-chains 146 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 364 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 373 THR 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 476 VAL Chi-restraints excluded: chain A residue 480 SER 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 142 ASP 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 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 76 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 0.0060 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.183213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144072 restraints weight = 9158.778| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.01 r_work: 0.3605 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2209 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= 0.131 Angle : 0.585 9.263 8889 Z= 0.295 Chirality : 0.046 0.254 1015 Planarity : 0.005 0.066 1141 Dihedral : 5.646 58.911 958 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.90 % Allowed : 28.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.29), residues: 795 helix: -1.60 (0.54), residues: 82 sheet: -1.44 (0.35), residues: 195 loop : -1.48 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 170 TYR 0.012 0.001 TYR J 62 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 covalent geometry : bond 0.00312 ( 6485) covalent geometry : angle 0.58099 ( 8841) SS BOND : bond 0.00246 ( 18) SS BOND : angle 0.77375 ( 36) hydrogen bonds : bond 0.03613 ( 151) hydrogen bonds : angle 5.38326 ( 462) link_BETA1-4 : bond 0.00343 ( 1) link_BETA1-4 : angle 0.57175 ( 3) link_NAG-ASN : bond 0.00314 ( 3) link_NAG-ASN : angle 1.90440 ( 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 152 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 414 CYS cc_start: 0.5612 (OUTLIER) cc_final: 0.5275 (t) REVERT: A 570 ASP cc_start: 0.7020 (t0) cc_final: 0.6719 (t0) REVERT: L 382 TRP cc_start: 0.6153 (m100) cc_final: 0.5247 (m100) REVERT: L 490 GLN cc_start: 0.8064 (tp40) cc_final: 0.7493 (tp40) REVERT: L 515 TYR cc_start: 0.8486 (m-80) cc_final: 0.8025 (m-80) REVERT: L 534 TYR cc_start: 0.8317 (m-80) cc_final: 0.8076 (m-80) REVERT: J 11 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7573 (mmtm) outliers start: 35 outliers final: 22 residues processed: 145 average time/residue: 0.0771 time to fit residues: 14.5850 Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 414 CYS Chi-restraints excluded: chain A residue 441 ILE 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 496 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 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 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 88 SER 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: 0.2980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 0.0050 chunk 42 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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** L 400 HIS J 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.184130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145036 restraints weight = 9110.562| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.02 r_work: 0.3612 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2305 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= 0.118 Angle : 0.570 9.527 8889 Z= 0.287 Chirality : 0.045 0.237 1015 Planarity : 0.005 0.066 1141 Dihedral : 5.374 58.635 958 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.03 % Allowed : 28.39 % Favored : 66.57 % 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 aren not related in a simple way. whole: -2.01 (0.29), residues: 795 helix: -1.47 (0.56), residues: 82 sheet: -1.22 (0.37), residues: 185 loop : -1.39 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 211 TYR 0.014 0.001 TYR J 62 PHE 0.018 0.001 PHE M 295 TRP 0.013 0.001 TRP A 382 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6485) covalent geometry : angle 0.56663 ( 8841) SS BOND : bond 0.00197 ( 18) SS BOND : angle 0.71536 ( 36) hydrogen bonds : bond 0.03424 ( 151) hydrogen bonds : angle 5.17050 ( 462) link_BETA1-4 : bond 0.00363 ( 1) link_BETA1-4 : angle 0.62938 ( 3) link_NAG-ASN : bond 0.00286 ( 3) link_NAG-ASN : angle 1.70289 ( 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 152 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 414 CYS cc_start: 0.5558 (OUTLIER) cc_final: 0.5188 (t) REVERT: A 570 ASP cc_start: 0.7005 (t0) cc_final: 0.6719 (t0) REVERT: L 382 TRP cc_start: 0.6127 (m100) cc_final: 0.5190 (m100) REVERT: L 490 GLN cc_start: 0.8099 (tp40) cc_final: 0.7856 (tp40) REVERT: L 515 TYR cc_start: 0.8395 (m-80) cc_final: 0.7900 (m-80) REVERT: M 277 GLU cc_start: 0.7244 (pm20) cc_final: 0.6528 (pm20) REVERT: J 11 LYS cc_start: 0.7733 (mmtm) cc_final: 0.7512 (mmtm) outliers start: 36 outliers final: 24 residues processed: 143 average time/residue: 0.0813 time to fit residues: 15.0873 Evaluate side-chains 129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 480 SER 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 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 251 ASN 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 18 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 Chi-restraints excluded: chain J residue 89 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** J 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.180885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143560 restraints weight = 9031.982| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.86 r_work: 0.3595 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6507 Z= 0.140 Angle : 0.600 10.051 8889 Z= 0.302 Chirality : 0.045 0.239 1015 Planarity : 0.005 0.066 1141 Dihedral : 5.428 58.721 958 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.03 % Allowed : 28.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.29), residues: 795 helix: -1.46 (0.55), residues: 82 sheet: -1.18 (0.37), residues: 185 loop : -1.36 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 314 TYR 0.022 0.001 TYR M 301 PHE 0.012 0.001 PHE A 354 TRP 0.014 0.001 TRP A 382 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6485) covalent geometry : angle 0.59713 ( 8841) SS BOND : bond 0.00284 ( 18) SS BOND : angle 0.73741 ( 36) hydrogen bonds : bond 0.03382 ( 151) hydrogen bonds : angle 5.11432 ( 462) link_BETA1-4 : bond 0.00332 ( 1) link_BETA1-4 : angle 0.66337 ( 3) link_NAG-ASN : bond 0.00255 ( 3) link_NAG-ASN : angle 1.81689 ( 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 146 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.149 Fit side-chains REVERT: A 414 CYS cc_start: 0.5556 (OUTLIER) cc_final: 0.5184 (t) REVERT: A 467 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7888 (mmt180) REVERT: A 570 ASP cc_start: 0.7100 (t0) cc_final: 0.6821 (t0) REVERT: L 382 TRP cc_start: 0.6136 (m100) cc_final: 0.5243 (m100) REVERT: L 490 GLN cc_start: 0.8096 (tp40) cc_final: 0.7615 (tp40) REVERT: L 515 TYR cc_start: 0.8431 (m-80) cc_final: 0.7872 (m-80) REVERT: L 534 TYR cc_start: 0.8332 (m-80) cc_final: 0.8114 (m-80) REVERT: M 157 ASN cc_start: 0.8630 (t0) cc_final: 0.8410 (t0) REVERT: M 277 GLU cc_start: 0.7272 (pm20) cc_final: 0.6527 (pm20) REVERT: J 11 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7482 (mmtm) outliers start: 36 outliers final: 27 residues processed: 135 average time/residue: 0.0749 time to fit residues: 13.1983 Evaluate side-chains 134 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 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 371 ASP 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 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 278 ASP 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 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 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: 0.0030 chunk 25 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.182342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.144472 restraints weight = 9190.174| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.96 r_work: 0.3605 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2532 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= 0.144 Angle : 0.599 9.774 8889 Z= 0.300 Chirality : 0.046 0.241 1015 Planarity : 0.005 0.065 1141 Dihedral : 5.380 59.296 958 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.29), residues: 795 helix: -1.42 (0.55), residues: 82 sheet: -1.12 (0.37), residues: 186 loop : -1.36 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 314 TYR 0.021 0.001 TYR J 62 PHE 0.016 0.002 PHE M 295 TRP 0.015 0.001 TRP A 382 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6485) covalent geometry : angle 0.59588 ( 8841) SS BOND : bond 0.00280 ( 18) SS BOND : angle 0.75514 ( 36) hydrogen bonds : bond 0.03362 ( 151) hydrogen bonds : angle 5.09503 ( 462) link_BETA1-4 : bond 0.00316 ( 1) link_BETA1-4 : angle 0.62205 ( 3) link_NAG-ASN : bond 0.00265 ( 3) link_NAG-ASN : angle 1.82993 ( 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 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.149 Fit side-chains REVERT: A 414 CYS cc_start: 0.5539 (OUTLIER) cc_final: 0.5177 (t) REVERT: A 467 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7832 (mmt180) REVERT: L 382 TRP cc_start: 0.6233 (m100) cc_final: 0.5413 (m100) REVERT: L 490 GLN cc_start: 0.8065 (tp40) cc_final: 0.7556 (tp40) REVERT: L 515 TYR cc_start: 0.8464 (m-80) cc_final: 0.7998 (m-80) REVERT: L 534 TYR cc_start: 0.8297 (m-80) cc_final: 0.8045 (m-80) REVERT: M 277 GLU cc_start: 0.7249 (pm20) cc_final: 0.6613 (pm20) outliers start: 32 outliers final: 26 residues processed: 128 average time/residue: 0.0711 time to fit residues: 12.1335 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 476 VAL Chi-restraints excluded: chain A residue 480 SER 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 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 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 278 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.181595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143528 restraints weight = 9299.213| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.98 r_work: 0.3592 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2649 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= 0.157 Angle : 0.608 9.948 8889 Z= 0.305 Chirality : 0.046 0.242 1015 Planarity : 0.005 0.065 1141 Dihedral : 5.408 60.490 958 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.76 % Allowed : 29.09 % Favored : 66.15 % 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 aren not related in a simple way. whole: -1.94 (0.30), residues: 795 helix: -1.43 (0.55), residues: 82 sheet: -1.13 (0.38), residues: 186 loop : -1.35 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 314 TYR 0.022 0.001 TYR J 62 PHE 0.013 0.001 PHE A 354 TRP 0.017 0.001 TRP A 382 HIS 0.002 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6485) covalent geometry : angle 0.60519 ( 8841) SS BOND : bond 0.00318 ( 18) SS BOND : angle 0.75367 ( 36) hydrogen bonds : bond 0.03358 ( 151) hydrogen bonds : angle 5.12959 ( 462) link_BETA1-4 : bond 0.00278 ( 1) link_BETA1-4 : angle 0.61239 ( 3) link_NAG-ASN : bond 0.00271 ( 3) link_NAG-ASN : angle 1.83411 ( 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 143 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.170 Fit side-chains REVERT: A 414 CYS cc_start: 0.5545 (OUTLIER) cc_final: 0.5179 (t) REVERT: A 467 ARG cc_start: 0.8095 (mmm160) cc_final: 0.7828 (mmt180) REVERT: L 382 TRP cc_start: 0.6227 (m100) cc_final: 0.5336 (m100) REVERT: L 490 GLN cc_start: 0.8074 (tp40) cc_final: 0.7543 (tp40) REVERT: L 515 TYR cc_start: 0.8489 (m-80) cc_final: 0.8019 (m-80) REVERT: L 522 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8476 (p) REVERT: L 534 TYR cc_start: 0.8326 (m-80) cc_final: 0.8075 (m-80) REVERT: M 277 GLU cc_start: 0.7275 (pm20) cc_final: 0.6625 (pm20) outliers start: 34 outliers final: 25 residues processed: 134 average time/residue: 0.0809 time to fit residues: 14.2304 Evaluate side-chains 135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 476 VAL Chi-restraints excluded: chain A residue 480 SER 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 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 548 THR 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 268 VAL Chi-restraints excluded: chain M residue 278 ASP Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 341 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 3 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.181616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143440 restraints weight = 9151.034| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.97 r_work: 0.3595 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6507 Z= 0.158 Angle : 0.617 11.048 8889 Z= 0.308 Chirality : 0.046 0.236 1015 Planarity : 0.005 0.065 1141 Dihedral : 5.433 61.459 958 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.34 % Allowed : 29.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.30), residues: 795 helix: -1.48 (0.54), residues: 82 sheet: -1.11 (0.38), residues: 186 loop : -1.36 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 314 TYR 0.021 0.001 TYR J 62 PHE 0.015 0.002 PHE M 295 TRP 0.017 0.001 TRP A 382 HIS 0.002 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6485) covalent geometry : angle 0.61432 ( 8841) SS BOND : bond 0.00321 ( 18) SS BOND : angle 0.73525 ( 36) hydrogen bonds : bond 0.03358 ( 151) hydrogen bonds : angle 5.10670 ( 462) link_BETA1-4 : bond 0.00287 ( 1) link_BETA1-4 : angle 0.57283 ( 3) link_NAG-ASN : bond 0.00262 ( 3) link_NAG-ASN : angle 1.75828 ( 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 141 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.202 Fit side-chains REVERT: A 414 CYS cc_start: 0.5540 (OUTLIER) cc_final: 0.5160 (t) REVERT: A 467 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7794 (mmt180) REVERT: L 382 TRP cc_start: 0.6214 (m100) cc_final: 0.5315 (m100) REVERT: L 490 GLN cc_start: 0.8076 (tp40) cc_final: 0.7562 (tp40) REVERT: L 515 TYR cc_start: 0.8496 (m-80) cc_final: 0.7993 (m-80) REVERT: L 522 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8499 (p) REVERT: L 534 TYR cc_start: 0.8292 (m-80) cc_final: 0.8033 (m-80) REVERT: M 170 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7243 (mtm180) REVERT: M 277 GLU cc_start: 0.7277 (pm20) cc_final: 0.6619 (pm20) outliers start: 31 outliers final: 26 residues processed: 134 average time/residue: 0.0679 time to fit residues: 11.8510 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 : 0.140 ------------------------------------------------------------------------------- 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 476 VAL Chi-restraints excluded: chain A residue 480 SER 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 371 ASP 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 522 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 548 THR 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 268 VAL Chi-restraints excluded: chain M residue 278 ASP Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 341 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN J 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.181336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143647 restraints weight = 9138.949| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.91 r_work: 0.3601 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6507 Z= 0.159 Angle : 0.636 12.599 8889 Z= 0.317 Chirality : 0.046 0.231 1015 Planarity : 0.005 0.065 1141 Dihedral : 5.468 61.710 958 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.48 % Allowed : 28.95 % Favored : 66.57 % 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 aren not related in a simple way. whole: -1.93 (0.30), residues: 795 helix: -1.47 (0.54), residues: 82 sheet: -1.08 (0.39), residues: 186 loop : -1.36 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 314 TYR 0.021 0.001 TYR J 62 PHE 0.013 0.001 PHE A 354 TRP 0.037 0.002 TRP A 382 HIS 0.002 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6485) covalent geometry : angle 0.62627 ( 8841) SS BOND : bond 0.00385 ( 18) SS BOND : angle 1.71218 ( 36) hydrogen bonds : bond 0.03316 ( 151) hydrogen bonds : angle 5.12486 ( 462) link_BETA1-4 : bond 0.00430 ( 1) link_BETA1-4 : angle 0.57670 ( 3) link_NAG-ASN : bond 0.00252 ( 3) link_NAG-ASN : angle 1.71543 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.29 seconds wall clock time: 30 minutes 9.62 seconds (1809.62 seconds total)