Starting phenix.real_space_refine on Tue Feb 11 17:16:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wys_37937/02_2025/8wys_37937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wys_37937/02_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_37937/02_2025/8wys_37937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wys_37937/02_2025/8wys_37937.map" model { file = "/net/cci-nas-00/data/ceres_data/8wys_37937/02_2025/8wys_37937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wys_37937/02_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-5592/modules/chem_data/mon_lib" Total number of atoms: 6340 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "L" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "M" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1669 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain: "J" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.30, per 1000 atoms: 0.84 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: 1.36 Conformation dependent library (CDL) restraints added in 882.4 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: 0.80 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: 2.15 Time building geometry restraints manager: 1.61 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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- 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 : 0.735 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: 0.2254 time to fit residues: 35.4068 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 : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 83 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.185963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147709 restraints weight = 9107.772| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.01 r_work: 0.3642 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6485 Z= 0.231 Angle : 0.590 11.674 8841 Z= 0.304 Chirality : 0.045 0.270 1015 Planarity : 0.006 0.080 1141 Dihedral : 6.045 52.563 961 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.17 % Allowed : 26.43 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.28), residues: 795 helix: -2.71 (0.41), residues: 87 sheet: -1.52 (0.36), residues: 190 loop : -1.70 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 382 HIS 0.003 0.001 HIS A 450 PHE 0.013 0.001 PHE A 354 TYR 0.012 0.001 TYR A 375 ARG 0.006 0.000 ARG J 16 *********************** 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 : 0.691 Fit side-chains REVERT: A 367 CYS cc_start: 0.3820 (OUTLIER) cc_final: 0.2933 (p) REVERT: A 570 ASP cc_start: 0.7118 (t0) cc_final: 0.6884 (t0) REVERT: L 382 TRP cc_start: 0.5916 (m100) cc_final: 0.5144 (m100) REVERT: L 515 TYR cc_start: 0.8326 (m-80) cc_final: 0.7595 (m-80) outliers start: 37 outliers final: 19 residues processed: 146 average time/residue: 0.1968 time to fit residues: 37.8082 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 301 TYR Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 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 L 400 HIS L 490 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.184198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145859 restraints weight = 9269.774| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.02 r_work: 0.3618 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6485 Z= 0.232 Angle : 0.576 9.553 8841 Z= 0.296 Chirality : 0.046 0.259 1015 Planarity : 0.005 0.066 1141 Dihedral : 5.669 53.025 958 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.87 % Allowed : 24.62 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.28), residues: 795 helix: -2.16 (0.48), residues: 81 sheet: -1.48 (0.35), residues: 197 loop : -1.59 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.003 0.001 HIS M 155 PHE 0.013 0.001 PHE A 354 TYR 0.010 0.001 TYR A 562 ARG 0.003 0.000 ARG M 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1590 Ramachandran restraints generated. 795 Oldfield, 0 Emsley, 795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.677 Fit side-chains REVERT: A 367 CYS cc_start: 0.4081 (OUTLIER) cc_final: 0.3142 (p) REVERT: A 382 TRP cc_start: 0.3497 (m100) cc_final: 0.2978 (m100) REVERT: A 414 CYS cc_start: 0.5793 (OUTLIER) cc_final: 0.5381 (t) REVERT: A 570 ASP cc_start: 0.7125 (t0) cc_final: 0.6784 (t0) REVERT: L 382 TRP cc_start: 0.5997 (m100) cc_final: 0.5359 (m100) REVERT: L 515 TYR cc_start: 0.8401 (m-80) cc_final: 0.7745 (m-80) outliers start: 42 outliers final: 25 residues processed: 147 average time/residue: 0.1950 time to fit residues: 37.4261 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 : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 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** J 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.183353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145130 restraints weight = 9305.173| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.01 r_work: 0.3611 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1866 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= 0.227 Angle : 0.568 9.601 8841 Z= 0.289 Chirality : 0.045 0.250 1015 Planarity : 0.005 0.065 1141 Dihedral : 5.513 55.280 958 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.59 % Allowed : 26.29 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.29), residues: 795 helix: -1.79 (0.51), residues: 82 sheet: -1.45 (0.34), residues: 210 loop : -1.52 (0.28), 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 0.014 0.001 PHE A 354 TYR 0.011 0.001 TYR A 562 ARG 0.003 0.000 ARG M 211 *********************** 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 157 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.715 Fit side-chains REVERT: A 367 CYS cc_start: 0.4122 (OUTLIER) cc_final: 0.3492 (p) REVERT: A 382 TRP cc_start: 0.3570 (m100) cc_final: 0.2973 (m100) REVERT: A 414 CYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5323 (t) REVERT: A 570 ASP cc_start: 0.7078 (t0) cc_final: 0.6800 (t0) REVERT: L 382 TRP cc_start: 0.6031 (m100) cc_final: 0.5339 (m100) REVERT: L 515 TYR cc_start: 0.8418 (m-80) cc_final: 0.7788 (m-80) REVERT: M 192 ASN cc_start: 0.4966 (p0) cc_final: 0.4760 (p0) outliers start: 40 outliers final: 25 residues processed: 151 average time/residue: 0.2051 time to fit residues: 39.7626 Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 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 496 SER Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 340 ASP Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.0470 chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.181275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142848 restraints weight = 9177.759| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.00 r_work: 0.3590 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2088 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= 0.283 Angle : 0.601 9.704 8841 Z= 0.303 Chirality : 0.046 0.247 1015 Planarity : 0.005 0.062 1141 Dihedral : 5.623 57.841 958 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.45 % Allowed : 27.41 % Favored : 67.13 % 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: -2.22 (0.29), residues: 795 helix: -1.58 (0.54), residues: 82 sheet: -1.32 (0.35), residues: 200 loop : -1.55 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 167 HIS 0.004 0.001 HIS J 63 PHE 0.015 0.002 PHE A 354 TYR 0.013 0.001 TYR A 562 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 161 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.723 Fit side-chains REVERT: A 367 CYS cc_start: 0.4368 (OUTLIER) cc_final: 0.3702 (p) REVERT: A 414 CYS cc_start: 0.5745 (OUTLIER) cc_final: 0.5307 (t) REVERT: A 570 ASP cc_start: 0.7212 (t0) cc_final: 0.6880 (t0) REVERT: L 382 TRP cc_start: 0.6051 (m100) cc_final: 0.5292 (m100) REVERT: L 515 TYR cc_start: 0.8474 (m-80) cc_final: 0.7857 (m-80) outliers start: 39 outliers final: 28 residues processed: 152 average time/residue: 0.1930 time to fit residues: 38.1482 Evaluate side-chains 142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 142 ASP Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 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 76 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 9 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.180250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141886 restraints weight = 9106.992| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.95 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: 0.7875 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6485 Z= 0.300 Angle : 0.630 10.034 8841 Z= 0.317 Chirality : 0.047 0.248 1015 Planarity : 0.005 0.060 1141 Dihedral : 5.714 61.472 958 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 6.15 % Allowed : 27.83 % 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: -2.26 (0.29), residues: 795 helix: -1.59 (0.53), residues: 89 sheet: -1.33 (0.35), residues: 199 loop : -1.59 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 382 HIS 0.004 0.001 HIS J 63 PHE 0.016 0.002 PHE M 295 TYR 0.014 0.001 TYR A 562 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: 44 poor density : 119 time to evaluate : 0.719 Fit side-chains REVERT: A 367 CYS cc_start: 0.4403 (OUTLIER) cc_final: 0.3793 (p) REVERT: A 414 CYS cc_start: 0.5650 (OUTLIER) cc_final: 0.5246 (t) REVERT: A 453 ASP cc_start: 0.6226 (t70) cc_final: 0.6013 (t70) REVERT: A 518 HIS cc_start: 0.7586 (m-70) cc_final: 0.7344 (m90) REVERT: A 570 ASP cc_start: 0.7184 (t0) cc_final: 0.6869 (t0) REVERT: L 382 TRP cc_start: 0.6025 (m100) cc_final: 0.5073 (m100) REVERT: L 515 TYR cc_start: 0.8522 (m-80) cc_final: 0.7907 (m-80) REVERT: M 157 ASN cc_start: 0.8543 (t0) cc_final: 0.8289 (t0) REVERT: J 9 ASP cc_start: 0.8101 (t0) cc_final: 0.7899 (t0) outliers start: 44 outliers final: 26 residues processed: 153 average time/residue: 0.2007 time to fit residues: 40.0668 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 : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 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 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 483 ASP Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 142 ASP Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 76 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.0020 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.182723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144563 restraints weight = 9220.764| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.99 r_work: 0.3608 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.003 0.038 6485 Z= 0.212 Angle : 0.589 9.504 8841 Z= 0.296 Chirality : 0.045 0.227 1015 Planarity : 0.005 0.061 1141 Dihedral : 5.449 60.516 958 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.45 % Allowed : 28.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.29), residues: 795 helix: -1.43 (0.55), residues: 82 sheet: -1.26 (0.35), residues: 200 loop : -1.49 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 382 HIS 0.003 0.001 HIS A 518 PHE 0.012 0.001 PHE A 354 TYR 0.009 0.001 TYR A 375 ARG 0.004 0.000 ARG M 170 *********************** 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 156 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.681 Fit side-chains REVERT: A 367 CYS cc_start: 0.4087 (OUTLIER) cc_final: 0.3395 (p) REVERT: A 414 CYS cc_start: 0.5652 (OUTLIER) cc_final: 0.5268 (t) REVERT: A 570 ASP cc_start: 0.7071 (t0) cc_final: 0.6834 (t0) REVERT: L 382 TRP cc_start: 0.6064 (m100) cc_final: 0.5185 (m100) REVERT: L 515 TYR cc_start: 0.8500 (m-80) cc_final: 0.7882 (m-80) REVERT: M 170 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7238 (mtm180) REVERT: M 277 GLU cc_start: 0.7217 (pm20) cc_final: 0.6603 (pm20) outliers start: 39 outliers final: 24 residues processed: 146 average time/residue: 0.1961 time to fit residues: 37.5012 Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 543 LEU Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.180347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141931 restraints weight = 9106.312| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.94 r_work: 0.3579 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6485 Z= 0.303 Angle : 0.627 10.233 8841 Z= 0.315 Chirality : 0.047 0.238 1015 Planarity : 0.005 0.059 1141 Dihedral : 5.660 61.808 958 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.48 % Allowed : 28.67 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.29), residues: 795 helix: -1.42 (0.55), residues: 82 sheet: -1.27 (0.36), residues: 199 loop : -1.50 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 382 HIS 0.003 0.001 HIS J 63 PHE 0.016 0.002 PHE A 354 TYR 0.011 0.001 TYR A 562 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 147 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.634 Fit side-chains REVERT: A 367 CYS cc_start: 0.4195 (OUTLIER) cc_final: 0.3579 (p) REVERT: A 414 CYS cc_start: 0.5678 (OUTLIER) cc_final: 0.5259 (t) REVERT: A 467 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7865 (mmt180) REVERT: A 570 ASP cc_start: 0.7148 (t0) cc_final: 0.6922 (t0) REVERT: L 382 TRP cc_start: 0.6074 (m100) cc_final: 0.5220 (m100) REVERT: M 157 ASN cc_start: 0.8491 (t0) cc_final: 0.8266 (t0) REVERT: M 170 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7272 (mtm180) REVERT: M 227 THR cc_start: 0.8394 (m) cc_final: 0.8182 (m) REVERT: M 277 GLU cc_start: 0.7253 (pm20) cc_final: 0.6605 (pm20) REVERT: J 9 ASP cc_start: 0.8159 (t0) cc_final: 0.7933 (t0) outliers start: 32 outliers final: 24 residues processed: 139 average time/residue: 0.1978 time to fit residues: 35.7020 Evaluate side-chains 136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 543 LEU Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 339 GLU Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 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: 1.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.181680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143438 restraints weight = 9269.133| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.95 r_work: 0.3598 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2629 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= 0.245 Angle : 0.609 9.856 8841 Z= 0.306 Chirality : 0.046 0.220 1015 Planarity : 0.005 0.060 1141 Dihedral : 5.561 61.752 958 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.76 % Allowed : 28.25 % Favored : 66.99 % 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 (0.30), residues: 795 helix: -1.47 (0.54), residues: 82 sheet: -1.15 (0.38), residues: 186 loop : -1.38 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 382 HIS 0.003 0.001 HIS J 63 PHE 0.013 0.001 PHE A 354 TYR 0.009 0.001 TYR A 562 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 149 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.747 Fit side-chains REVERT: A 367 CYS cc_start: 0.4148 (OUTLIER) cc_final: 0.3454 (p) REVERT: A 414 CYS cc_start: 0.5641 (OUTLIER) cc_final: 0.5265 (t) REVERT: A 467 ARG cc_start: 0.8120 (mmm160) cc_final: 0.7870 (mmt180) REVERT: A 570 ASP cc_start: 0.7046 (t0) cc_final: 0.6826 (t0) REVERT: L 382 TRP cc_start: 0.6059 (m100) cc_final: 0.5183 (m100) REVERT: M 157 ASN cc_start: 0.8483 (t0) cc_final: 0.8266 (t0) REVERT: M 170 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7218 (mtm180) REVERT: M 277 GLU cc_start: 0.7278 (pm20) cc_final: 0.6617 (pm20) REVERT: J 9 ASP cc_start: 0.8166 (t0) cc_final: 0.7945 (t0) outliers start: 34 outliers final: 26 residues processed: 140 average time/residue: 0.1978 time to fit residues: 35.9741 Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 414 CYS Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain M residue 147 CYS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 251 ASN Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 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 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.0470 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.181654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143319 restraints weight = 9328.560| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.99 r_work: 0.3597 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2748 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= 0.247 Angle : 0.627 11.348 8841 Z= 0.313 Chirality : 0.046 0.216 1015 Planarity : 0.005 0.061 1141 Dihedral : 4.884 26.671 955 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.62 % Allowed : 28.95 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.30), residues: 795 helix: -1.48 (0.53), residues: 82 sheet: -1.08 (0.39), residues: 186 loop : -1.34 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 382 HIS 0.003 0.001 HIS J 63 PHE 0.016 0.002 PHE M 295 TYR 0.009 0.001 TYR A 562 ARG 0.004 0.000 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 148 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.738 Fit side-chains REVERT: A 367 CYS cc_start: 0.4224 (OUTLIER) cc_final: 0.3914 (p) REVERT: A 382 TRP cc_start: 0.4048 (m100) cc_final: 0.3836 (m100) REVERT: A 414 CYS cc_start: 0.5638 (OUTLIER) cc_final: 0.5251 (t) REVERT: A 467 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7868 (mmt180) REVERT: A 570 ASP cc_start: 0.6935 (t0) cc_final: 0.6710 (t0) REVERT: L 382 TRP cc_start: 0.6078 (m100) cc_final: 0.5195 (m100) REVERT: L 515 TYR cc_start: 0.8477 (m-80) cc_final: 0.8273 (m-80) REVERT: M 157 ASN cc_start: 0.8499 (t0) cc_final: 0.8289 (t0) REVERT: M 170 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7209 (mtm180) REVERT: M 277 GLU cc_start: 0.7293 (pm20) cc_final: 0.6616 (pm20) REVERT: J 9 ASP cc_start: 0.8194 (t0) cc_final: 0.7987 (t0) outliers start: 33 outliers final: 25 residues processed: 141 average time/residue: 0.2008 time to fit residues: 36.8634 Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 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 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 341 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 76 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.179582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141329 restraints weight = 9224.593| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.91 r_work: 0.3568 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6485 Z= 0.262 Angle : 0.624 10.659 8841 Z= 0.311 Chirality : 0.047 0.216 1015 Planarity : 0.005 0.061 1141 Dihedral : 4.931 26.769 955 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.20 % Allowed : 29.09 % Favored : 66.71 % 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: -1.48 (0.53), residues: 82 sheet: -1.06 (0.39), residues: 186 loop : -1.36 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 382 HIS 0.003 0.001 HIS J 63 PHE 0.014 0.001 PHE A 354 TYR 0.016 0.001 TYR A 375 ARG 0.005 0.000 ARG M 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.78 seconds wall clock time: 62 minutes 32.77 seconds (3752.77 seconds total)