Starting phenix.real_space_refine on Tue Mar 11 16:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wys_37937/03_2025/8wys_37937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wys_37937/03_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_37937/03_2025/8wys_37937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wys_37937/03_2025/8wys_37937.map" model { file = "/net/cci-nas-00/data/ceres_data/8wys_37937/03_2025/8wys_37937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wys_37937/03_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-5624/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: 4.84, per 1000 atoms: 0.76 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: 1.37 Conformation dependent library (CDL) restraints added in 942.8 milliseconds 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1518 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 20 sheets defined 12.2% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 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: 2.03 Time building geometry restraints manager: 1.67 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: 2.540 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.460 Find NCS groups from input model: 0.160 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- 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 6485 Z= 0.367 Angle : 0.916 13.792 8841 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 *********************** 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 : 0.710 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: 0.2068 time to fit residues: 32.6410 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 : 0.723 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.186412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148221 restraints weight = 9097.753| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.01 r_work: 0.3649 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6485 Z= 0.221 Angle : 0.586 11.806 8841 Z= 0.301 Chirality : 0.045 0.268 1015 Planarity : 0.006 0.081 1141 Dihedral : 6.039 52.864 961 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % 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: -2.63 (0.28), residues: 795 helix: -2.71 (0.42), 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 0.011 0.001 TRP A 418 HIS 0.002 0.001 HIS M 337 PHE 0.012 0.001 PHE L 479 TYR 0.012 0.001 TYR A 375 ARG 0.004 0.000 ARG J 16 *********************** 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 : 0.754 Fit side-chains REVERT: A 367 CYS cc_start: 0.3815 (OUTLIER) cc_final: 0.2925 (p) REVERT: A 570 ASP cc_start: 0.7101 (t0) cc_final: 0.6866 (t0) REVERT: L 382 TRP cc_start: 0.5905 (m100) cc_final: 0.5139 (m100) REVERT: L 515 TYR cc_start: 0.8319 (m-80) cc_final: 0.7580 (m-80) REVERT: J 11 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7385 (mmtm) outliers start: 37 outliers final: 20 residues processed: 146 average time/residue: 0.1861 time to fit residues: 35.7993 Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 L 400 HIS J 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.180386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.141599 restraints weight = 9286.159| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.01 r_work: 0.3573 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6485 Z= 0.351 Angle : 0.642 10.093 8841 Z= 0.330 Chirality : 0.048 0.277 1015 Planarity : 0.005 0.066 1141 Dihedral : 6.009 55.758 958 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.57 % Allowed : 24.76 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.51 (0.28), residues: 795 helix: -2.17 (0.48), residues: 82 sheet: -1.52 (0.34), residues: 211 loop : -1.67 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.004 0.001 HIS A 518 PHE 0.017 0.002 PHE A 354 TYR 0.016 0.002 TYR A 562 ARG 0.003 0.000 ARG A 443 *********************** 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 166 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.700 Fit side-chains REVERT: A 367 CYS cc_start: 0.4592 (OUTLIER) cc_final: 0.3952 (p) REVERT: A 382 TRP cc_start: 0.3615 (m100) cc_final: 0.3091 (m100) REVERT: A 414 CYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5306 (t) REVERT: A 570 ASP cc_start: 0.7251 (t0) cc_final: 0.6914 (t0) REVERT: L 382 TRP cc_start: 0.6018 (m100) cc_final: 0.5268 (m100) REVERT: L 490 GLN cc_start: 0.8097 (tp40) cc_final: 0.7786 (tp40) REVERT: L 515 TYR cc_start: 0.8478 (m-80) cc_final: 0.7837 (m-80) REVERT: J 11 LYS cc_start: 0.7840 (mmtm) cc_final: 0.7551 (mmtm) outliers start: 47 outliers final: 24 residues processed: 156 average time/residue: 0.2423 time to fit residues: 49.1536 Evaluate side-chains 140 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 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 175 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 0.0870 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145065 restraints weight = 9288.503| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.01 r_work: 0.3616 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6485 Z= 0.195 Angle : 0.571 9.190 8841 Z= 0.289 Chirality : 0.045 0.251 1015 Planarity : 0.005 0.064 1141 Dihedral : 5.597 57.175 958 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.48 % Allowed : 27.27 % 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 (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: -1.79 (0.52), residues: 82 sheet: -1.46 (0.34), residues: 210 loop : -1.54 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.005 0.001 HIS A 450 PHE 0.013 0.001 PHE L 479 TYR 0.010 0.001 TYR J 62 ARG 0.004 0.000 ARG M 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.837 Fit side-chains REVERT: A 367 CYS cc_start: 0.4153 (OUTLIER) cc_final: 0.3836 (p) REVERT: A 382 TRP cc_start: 0.3551 (m100) cc_final: 0.3037 (m100) REVERT: A 414 CYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5306 (t) REVERT: A 570 ASP cc_start: 0.6983 (t0) cc_final: 0.6700 (t0) REVERT: L 382 TRP cc_start: 0.6047 (m100) cc_final: 0.5343 (m100) REVERT: L 490 GLN cc_start: 0.7987 (tp40) cc_final: 0.7570 (tp40) REVERT: L 515 TYR cc_start: 0.8417 (m-80) cc_final: 0.7798 (m-80) REVERT: L 534 TYR cc_start: 0.8280 (m-80) cc_final: 0.8038 (m-80) REVERT: M 192 ASN cc_start: 0.5021 (p0) cc_final: 0.4800 (p0) REVERT: J 11 LYS cc_start: 0.7761 (mmtm) cc_final: 0.7505 (mmtm) outliers start: 32 outliers final: 22 residues processed: 148 average time/residue: 0.2227 time to fit residues: 43.2357 Evaluate side-chains 136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain 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 503 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 22 ILE Chi-restraints excluded: chain J residue 61 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 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 = 0.4158 r_free = 0.4158 target = 0.181130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142994 restraints weight = 9097.085| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.96 r_work: 0.3586 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6485 Z= 0.272 Angle : 0.604 9.266 8841 Z= 0.306 Chirality : 0.046 0.250 1015 Planarity : 0.005 0.061 1141 Dihedral : 5.645 58.711 958 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.45 % Allowed : 28.53 % Favored : 66.01 % 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: -2.24 (0.29), residues: 795 helix: -1.62 (0.52), residues: 89 sheet: -1.28 (0.35), residues: 200 loop : -1.58 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.004 0.001 HIS M 155 PHE 0.015 0.001 PHE A 354 TYR 0.014 0.001 TYR J 62 ARG 0.007 0.000 ARG M 314 *********************** 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 157 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 367 CYS cc_start: 0.4445 (OUTLIER) cc_final: 0.4206 (p) REVERT: A 414 CYS cc_start: 0.5691 (OUTLIER) cc_final: 0.5261 (t) REVERT: A 570 ASP cc_start: 0.7152 (t0) cc_final: 0.6818 (t0) REVERT: L 382 TRP cc_start: 0.6077 (m100) cc_final: 0.5279 (m100) REVERT: L 515 TYR cc_start: 0.8473 (m-80) cc_final: 0.7846 (m-80) REVERT: J 11 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7606 (mmtm) outliers start: 39 outliers final: 27 residues processed: 150 average time/residue: 0.2060 time to fit residues: 40.2824 Evaluate side-chains 139 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 251 ASN 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 22 ILE Chi-restraints excluded: chain J residue 30 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.180170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142871 restraints weight = 8941.602| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.85 r_work: 0.3585 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6485 Z= 0.242 Angle : 0.598 9.621 8841 Z= 0.301 Chirality : 0.045 0.243 1015 Planarity : 0.005 0.061 1141 Dihedral : 5.552 60.799 958 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 6.43 % Allowed : 27.13 % 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: -2.06 (0.29), residues: 795 helix: -1.45 (0.55), residues: 82 sheet: -1.25 (0.36), residues: 185 loop : -1.43 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 382 HIS 0.003 0.001 HIS J 63 PHE 0.016 0.002 PHE M 295 TYR 0.020 0.001 TYR L 534 ARG 0.005 0.000 ARG M 314 *********************** 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 163 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 414 CYS cc_start: 0.5654 (OUTLIER) cc_final: 0.5225 (t) REVERT: A 453 ASP cc_start: 0.6118 (OUTLIER) cc_final: 0.5884 (t70) REVERT: A 570 ASP cc_start: 0.7097 (t0) cc_final: 0.6775 (t0) REVERT: L 382 TRP cc_start: 0.5995 (m100) cc_final: 0.5107 (m100) REVERT: L 515 TYR cc_start: 0.8502 (m-80) cc_final: 0.7839 (m-80) REVERT: M 157 ASN cc_start: 0.8611 (t0) cc_final: 0.8358 (t0) REVERT: J 11 LYS cc_start: 0.7741 (mmtm) cc_final: 0.7497 (mmtm) outliers start: 46 outliers final: 26 residues processed: 152 average time/residue: 0.1792 time to fit residues: 35.7577 Evaluate side-chains 141 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR 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 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 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 18 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 71 CYS Chi-restraints excluded: chain J residue 76 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.0040 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.182135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144619 restraints weight = 9180.311| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.95 r_work: 0.3606 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6485 Z= 0.226 Angle : 0.599 10.179 8841 Z= 0.301 Chirality : 0.045 0.240 1015 Planarity : 0.005 0.060 1141 Dihedral : 5.438 60.526 958 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.31 % Allowed : 28.25 % 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: -2.00 (0.29), residues: 795 helix: -1.45 (0.55), residues: 82 sheet: -1.15 (0.37), residues: 185 loop : -1.41 (0.28), residues: 528 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 0.025 0.002 TYR M 301 ARG 0.004 0.000 ARG M 314 *********************** 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 155 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.714 Fit side-chains REVERT: A 414 CYS cc_start: 0.5665 (OUTLIER) cc_final: 0.5272 (t) REVERT: A 570 ASP cc_start: 0.7176 (t0) cc_final: 0.6933 (t0) REVERT: L 382 TRP cc_start: 0.6035 (m100) cc_final: 0.5232 (m100) REVERT: L 515 TYR cc_start: 0.8493 (m-80) cc_final: 0.7865 (m-80) REVERT: M 167 TRP cc_start: 0.7993 (t-100) cc_final: 0.7785 (t-100) REVERT: M 227 THR cc_start: 0.8306 (m) cc_final: 0.8087 (m) REVERT: M 277 GLU cc_start: 0.7232 (pm20) cc_final: 0.6616 (pm20) outliers start: 38 outliers final: 29 residues processed: 143 average time/residue: 0.1894 time to fit residues: 35.5046 Evaluate side-chains 141 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 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 417 ASP Chi-restraints excluded: chain L residue 493 GLN 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 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 A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.181515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143715 restraints weight = 9086.876| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.94 r_work: 0.3600 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6485 Z= 0.255 Angle : 0.611 10.206 8841 Z= 0.307 Chirality : 0.046 0.231 1015 Planarity : 0.005 0.060 1141 Dihedral : 5.514 61.020 958 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % 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: -1.97 (0.29), residues: 795 helix: -1.40 (0.55), residues: 82 sheet: -1.12 (0.37), residues: 186 loop : -1.40 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 382 HIS 0.003 0.001 HIS J 63 PHE 0.016 0.002 PHE M 295 TYR 0.028 0.002 TYR L 534 ARG 0.004 0.000 ARG M 314 *********************** 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 149 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.656 Fit side-chains REVERT: A 414 CYS cc_start: 0.5677 (OUTLIER) cc_final: 0.5270 (t) REVERT: A 570 ASP cc_start: 0.7247 (t0) cc_final: 0.6992 (t0) REVERT: L 382 TRP cc_start: 0.6039 (m100) cc_final: 0.5230 (m100) REVERT: L 515 TYR cc_start: 0.8522 (m-80) cc_final: 0.7872 (m-80) REVERT: M 157 ASN cc_start: 0.8462 (t0) cc_final: 0.8238 (t0) REVERT: M 277 GLU cc_start: 0.7246 (pm20) cc_final: 0.6619 (pm20) REVERT: M 291 LEU cc_start: 0.7701 (pt) cc_final: 0.7489 (pp) outliers start: 37 outliers final: 27 residues processed: 141 average time/residue: 0.1812 time to fit residues: 33.3391 Evaluate side-chains 136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR 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 417 ASP Chi-restraints excluded: chain L residue 493 GLN 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 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 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 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.183025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145220 restraints weight = 9239.563| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.94 r_work: 0.3615 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6485 Z= 0.228 Angle : 0.608 10.715 8841 Z= 0.303 Chirality : 0.045 0.225 1015 Planarity : 0.004 0.061 1141 Dihedral : 5.387 60.838 958 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.62 % Allowed : 29.09 % 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: -1.92 (0.30), residues: 795 helix: -1.40 (0.54), residues: 82 sheet: -1.18 (0.37), residues: 196 loop : -1.31 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 382 HIS 0.003 0.001 HIS A 518 PHE 0.012 0.001 PHE A 354 TYR 0.021 0.001 TYR L 534 ARG 0.004 0.000 ARG M 314 *********************** 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 144 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.735 Fit side-chains REVERT: A 414 CYS cc_start: 0.5597 (OUTLIER) cc_final: 0.5227 (t) REVERT: A 475 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8019 (mp) REVERT: L 382 TRP cc_start: 0.6064 (m100) cc_final: 0.5188 (m100) REVERT: L 515 TYR cc_start: 0.8514 (m-80) cc_final: 0.7987 (m-80) REVERT: M 157 ASN cc_start: 0.8476 (t0) cc_final: 0.8270 (t0) REVERT: M 277 GLU cc_start: 0.7279 (pm20) cc_final: 0.6612 (pm20) outliers start: 33 outliers final: 26 residues processed: 136 average time/residue: 0.1948 time to fit residues: 34.9701 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 475 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 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 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 268 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.176607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138592 restraints weight = 9148.833| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.85 r_work: 0.3530 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 6485 Z= 0.408 Angle : 0.692 10.975 8841 Z= 0.349 Chirality : 0.049 0.223 1015 Planarity : 0.005 0.060 1141 Dihedral : 5.254 27.882 955 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.48 % Allowed : 29.51 % Favored : 66.01 % 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: -1.48 (0.53), residues: 82 sheet: -1.15 (0.38), residues: 184 loop : -1.45 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 167 HIS 0.004 0.001 HIS J 63 PHE 0.018 0.002 PHE A 354 TYR 0.031 0.002 TYR L 534 ARG 0.004 0.001 ARG M 314 ********************** 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 145 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.639 Fit side-chains REVERT: A 414 CYS cc_start: 0.5677 (OUTLIER) cc_final: 0.5240 (t) REVERT: A 475 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7920 (mp) REVERT: A 518 HIS cc_start: 0.7675 (m-70) cc_final: 0.7299 (m90) REVERT: L 382 TRP cc_start: 0.6008 (m100) cc_final: 0.5040 (m100) REVERT: M 156 GLN cc_start: 0.7310 (pm20) cc_final: 0.6960 (pm20) REVERT: M 157 ASN cc_start: 0.8561 (t0) cc_final: 0.8332 (t0) REVERT: M 170 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7150 (mtm180) REVERT: M 277 GLU cc_start: 0.7342 (pm20) cc_final: 0.6543 (pm20) REVERT: M 340 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7981 (t70) outliers start: 32 outliers final: 22 residues processed: 138 average time/residue: 0.2061 time to fit residues: 36.5073 Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 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 493 GLN 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.181394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143674 restraints weight = 9216.971| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.89 r_work: 0.3597 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.003 0.038 6485 Z= 0.217 Angle : 0.620 10.498 8841 Z= 0.311 Chirality : 0.045 0.201 1015 Planarity : 0.004 0.061 1141 Dihedral : 4.839 26.355 955 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.64 % Allowed : 30.35 % Favored : 66.01 % 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: -1.93 (0.30), residues: 795 helix: -1.40 (0.54), residues: 82 sheet: -1.06 (0.39), residues: 187 loop : -1.39 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 382 HIS 0.003 0.001 HIS L 540 PHE 0.012 0.001 PHE L 479 TYR 0.019 0.001 TYR L 534 ARG 0.004 0.000 ARG M 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3626.38 seconds wall clock time: 62 minutes 49.20 seconds (3769.20 seconds total)