Starting phenix.real_space_refine on Fri Feb 14 19:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8s_18259/02_2025/8q8s_18259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8s_18259/02_2025/8q8s_18259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q8s_18259/02_2025/8q8s_18259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8s_18259/02_2025/8q8s_18259.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8s_18259/02_2025/8q8s_18259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8s_18259/02_2025/8q8s_18259.cif" } resolution = 2.68 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= 0.002 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 S 9 5.16 5 C 3258 2.51 5 N 963 2.21 5 O 972 1.98 5 H 5409 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 10611 Number of models: 1 Model: "" Number of chains: 9 Chain: "I" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "G" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "H" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 6.23, per 1000 atoms: 0.59 Number of scatterers: 10611 At special positions: 0 Unit cell: (142.492, 136.676, 44.347, 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) S 9 16.00 O 972 8.00 N 963 7.00 C 3258 6.00 H 5409 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 721.1 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.705A pdb=" N VAL I 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 317 through 321 Processing sheet with id=AA4, first strand: chain 'I' and resid 325 through 330 removed outlier: 7.061A pdb=" N GLY D 326 " --> pdb=" O LEU I 325 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN I 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 337 through 340 removed outlier: 6.552A pdb=" N GLU I 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'I' and resid 351 through 354 removed outlier: 6.450A pdb=" N GLN I 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE D 354 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS I 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 357 through 362 removed outlier: 6.634A pdb=" N LEU B 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE D 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 369 through 371 removed outlier: 6.493A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 374 through 378 removed outlier: 6.613A pdb=" N LYS I 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N PHE D 378 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR I 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 307 through 310 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.834A pdb=" N VAL C 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.506A pdb=" N LYS C 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N SER G 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL E 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LYS G 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER E 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330 removed outlier: 7.007A pdb=" N GLY G 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C 327 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLY E 326 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS G 329 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE E 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 340 removed outlier: 6.568A pdb=" N VAL E 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS G 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL E 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.581A pdb=" N GLN C 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE G 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS C 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.522A pdb=" N LEU E 357 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE G 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN E 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N HIS G 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR E 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 369 through 371 removed outlier: 6.523A pdb=" N LYS E 370 " --> pdb=" O ILE G 371 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 378 removed outlier: 6.553A pdb=" N LYS C 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE G 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR C 377 " --> pdb=" O PHE G 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 307 through 310 Processing sheet with id=AC2, first strand: chain 'F' and resid 313 through 314 Processing sheet with id=AC3, first strand: chain 'F' and resid 317 through 322 removed outlier: 6.494A pdb=" N VAL H 318 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LYS A 321 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER H 320 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 325 through 330 removed outlier: 5.959A pdb=" N GLY F 326 " --> pdb=" O ASN H 327 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N HIS H 329 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE F 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY H 326 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N HIS A 329 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE H 328 " --> pdb=" O HIS A 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 337 through 340 removed outlier: 6.610A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LYS H 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL F 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 351 through 354 Processing sheet with id=AC7, first strand: chain 'F' and resid 357 through 362 removed outlier: 6.558A pdb=" N LEU F 357 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE H 360 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN F 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N HIS H 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU H 357 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ILE A 360 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN H 359 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS A 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR H 361 " --> pdb=" O HIS A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 369 through 371 removed outlier: 6.506A pdb=" N LYS F 370 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS H 370 " --> pdb=" O ILE A 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 374 through 378 removed outlier: 6.497A pdb=" N HIS H 374 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR A 377 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU H 376 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 345 through 346 85 hydrogen bonds defined for protein. 255 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: 3.19 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 5400 1.12 - 1.29: 864 1.29 - 1.47: 1676 1.47 - 1.64: 2743 1.64 - 1.81: 9 Bond restraints: 10692 Sorted by residual: bond pdb=" N SER D 324 " pdb=" H SER D 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY D 323 " pdb=" H GLY D 323 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL B 363 " pdb=" H VAL B 363 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL D 363 " pdb=" H VAL D 363 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL I 363 " pdb=" H VAL I 363 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 10687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 15914 2.47 - 4.93: 2659 4.93 - 7.40: 819 7.40 - 9.86: 72 9.86 - 12.33: 12 Bond angle restraints: 19476 Sorted by residual: angle pdb=" N ASP H 348 " pdb=" CA ASP H 348 " pdb=" C ASP H 348 " ideal model delta sigma weight residual 110.23 120.21 -9.98 1.45e+00 4.76e-01 4.73e+01 angle pdb=" N SER F 341 " pdb=" CA SER F 341 " pdb=" C SER F 341 " ideal model delta sigma weight residual 108.45 116.16 -7.71 1.26e+00 6.30e-01 3.74e+01 angle pdb=" C SER F 341 " pdb=" N GLU F 342 " pdb=" CA GLU F 342 " ideal model delta sigma weight residual 123.27 134.23 -10.96 1.85e+00 2.92e-01 3.51e+01 angle pdb=" N GLN E 336 " pdb=" CA GLN E 336 " pdb=" C GLN E 336 " ideal model delta sigma weight residual 110.32 119.44 -9.12 1.59e+00 3.96e-01 3.29e+01 angle pdb=" N LYS C 343 " pdb=" CA LYS C 343 " pdb=" C LYS C 343 " ideal model delta sigma weight residual 110.23 118.15 -7.92 1.45e+00 4.76e-01 2.99e+01 ... (remaining 19471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4416 15.94 - 31.87: 227 31.87 - 47.81: 114 47.81 - 63.74: 130 63.74 - 79.67: 36 Dihedral angle restraints: 4923 sinusoidal: 2817 harmonic: 2106 Sorted by residual: dihedral pdb=" CA GLU A 342 " pdb=" C GLU A 342 " pdb=" N LYS A 343 " pdb=" CA LYS A 343 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" N GLN A 351 " pdb=" CA GLN A 351 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA LEU A 357 " pdb=" C LEU A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta harmonic sigma weight residual 180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 4920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 459 0.076 - 0.151: 260 0.151 - 0.226: 45 0.226 - 0.302: 19 0.302 - 0.377: 9 Chirality restraints: 792 Sorted by residual: chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ARG I 349 " pdb=" N ARG I 349 " pdb=" C ARG I 349 " pdb=" CB ARG I 349 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 789 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN H 336 " -0.070 2.00e-02 2.50e+03 6.38e-02 6.10e+01 pdb=" CD GLN H 336 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN H 336 " 0.046 2.00e-02 2.50e+03 pdb=" NE2 GLN H 336 " 0.049 2.00e-02 2.50e+03 pdb="HE21 GLN H 336 " 0.055 2.00e-02 2.50e+03 pdb="HE22 GLN H 336 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 368 " -0.058 2.00e-02 2.50e+03 5.56e-02 4.64e+01 pdb=" CG ASN D 368 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN D 368 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN D 368 " 0.069 2.00e-02 2.50e+03 pdb="HD21 ASN D 368 " 0.007 2.00e-02 2.50e+03 pdb="HD22 ASN D 368 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 310 " 0.080 2.00e-02 2.50e+03 3.55e-02 3.79e+01 pdb=" CG TYR H 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR H 310 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR H 310 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR H 310 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR H 310 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 310 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 310 " 0.049 2.00e-02 2.50e+03 pdb=" HD1 TYR H 310 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR H 310 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR H 310 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR H 310 " 0.026 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 730 2.16 - 2.77: 17642 2.77 - 3.38: 28361 3.38 - 3.99: 36626 3.99 - 4.60: 52989 Nonbonded interactions: 136348 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.555 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.558 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.576 2.450 ... (remaining 136343 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 8.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 25.670 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 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 : 0.011 0.038 5283 Z= 0.774 Angle : 2.114 10.964 7065 Z= 1.379 Chirality : 0.099 0.377 792 Planarity : 0.011 0.087 900 Dihedral : 9.516 77.054 2025 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.51 % 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: -1.68 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.005 HIS B 330 PHE 0.056 0.012 PHE F 378 TYR 0.077 0.023 TYR D 310 ARG 0.006 0.001 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 369 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7613 (mtmm) REVERT: I 375 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7478 (ttpp) REVERT: D 321 LYS cc_start: 0.7539 (mttt) cc_final: 0.7286 (ttmm) REVERT: D 338 GLU cc_start: 0.6586 (tt0) cc_final: 0.6254 (tt0) REVERT: D 358 ASP cc_start: 0.7678 (m-30) cc_final: 0.7434 (m-30) REVERT: C 353 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7253 (mmpt) REVERT: C 369 LYS cc_start: 0.7228 (mtpt) cc_final: 0.6961 (mttm) REVERT: E 369 LYS cc_start: 0.7279 (mtpt) cc_final: 0.7026 (mttp) REVERT: F 321 LYS cc_start: 0.7867 (mttt) cc_final: 0.7559 (ttmm) REVERT: F 375 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7174 (tttt) REVERT: G 321 LYS cc_start: 0.7686 (mttt) cc_final: 0.7444 (mttt) REVERT: G 369 LYS cc_start: 0.7054 (mtpt) cc_final: 0.6727 (mttm) REVERT: H 315 LEU cc_start: 0.8046 (mt) cc_final: 0.7779 (mt) REVERT: H 321 LYS cc_start: 0.7834 (mttt) cc_final: 0.7409 (mttm) REVERT: H 344 LEU cc_start: 0.6579 (mt) cc_final: 0.6331 (mp) REVERT: H 369 LYS cc_start: 0.7471 (mtpt) cc_final: 0.7185 (mtpp) REVERT: A 331 LYS cc_start: 0.7719 (mtpt) cc_final: 0.7438 (tmtt) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 2.8488 time to fit residues: 587.4773 Evaluate side-chains 112 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN D 368 ASN D 374 HIS F 307 GLN F 368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.176089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.154086 restraints weight = 17895.429| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 1.82 r_work: 0.4244 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5283 Z= 0.306 Angle : 0.743 6.445 7065 Z= 0.401 Chirality : 0.050 0.151 792 Planarity : 0.004 0.035 900 Dihedral : 7.157 28.141 702 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.53 % Allowed : 14.31 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 374 PHE 0.007 0.002 PHE B 346 TYR 0.011 0.003 TYR D 310 ARG 0.006 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8534 (mt) cc_final: 0.8209 (mm) REVERT: I 317 LYS cc_start: 0.7763 (pttt) cc_final: 0.7456 (ptpt) REVERT: I 349 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7153 (mtp180) REVERT: I 369 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7872 (mtmm) REVERT: B 311 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7961 (tmmt) REVERT: B 340 LYS cc_start: 0.7879 (tttm) cc_final: 0.7490 (ttmp) REVERT: B 349 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7078 (mtp180) REVERT: B 351 GLN cc_start: 0.8054 (tt0) cc_final: 0.7710 (mt0) REVERT: D 321 LYS cc_start: 0.7758 (mttt) cc_final: 0.7464 (ttmm) REVERT: D 338 GLU cc_start: 0.7032 (tt0) cc_final: 0.6790 (tt0) REVERT: C 353 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7480 (mmtt) REVERT: C 369 LYS cc_start: 0.7538 (mtpt) cc_final: 0.7140 (mttm) REVERT: E 369 LYS cc_start: 0.7515 (mtpt) cc_final: 0.7200 (mttp) REVERT: F 375 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7788 (tptt) REVERT: G 321 LYS cc_start: 0.7889 (mttt) cc_final: 0.7381 (tttt) REVERT: G 369 LYS cc_start: 0.7417 (mtpt) cc_final: 0.7037 (mttm) REVERT: H 315 LEU cc_start: 0.8032 (mt) cc_final: 0.7697 (mt) REVERT: H 344 LEU cc_start: 0.7171 (mt) cc_final: 0.6893 (mt) REVERT: H 345 ASP cc_start: 0.6377 (t0) cc_final: 0.6060 (m-30) REVERT: H 353 LYS cc_start: 0.7369 (mtpp) cc_final: 0.7054 (ttpp) REVERT: H 369 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7689 (mtpp) REVERT: A 338 GLU cc_start: 0.5453 (mm-30) cc_final: 0.5166 (mm-30) REVERT: A 369 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7647 (mttp) outliers start: 15 outliers final: 4 residues processed: 129 average time/residue: 2.9399 time to fit residues: 392.6639 Evaluate side-chains 104 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.173748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.151110 restraints weight = 17386.689| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 1.88 r_work: 0.4219 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5283 Z= 0.218 Angle : 0.641 6.676 7065 Z= 0.349 Chirality : 0.051 0.147 792 Planarity : 0.004 0.039 900 Dihedral : 6.459 21.807 702 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.69 % Allowed : 16.16 % Favored : 81.14 % 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: -2.50 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 330 PHE 0.006 0.001 PHE A 346 TYR 0.013 0.002 TYR D 310 ARG 0.007 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8550 (mt) cc_final: 0.8227 (mm) REVERT: I 317 LYS cc_start: 0.7715 (pttt) cc_final: 0.7405 (ptpt) REVERT: I 349 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6978 (mtp180) REVERT: I 369 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7884 (mtmm) REVERT: B 340 LYS cc_start: 0.7886 (tttm) cc_final: 0.7493 (ttmp) REVERT: B 351 GLN cc_start: 0.7971 (tt0) cc_final: 0.7663 (mt0) REVERT: D 321 LYS cc_start: 0.7780 (mttt) cc_final: 0.7537 (ttmm) REVERT: D 331 LYS cc_start: 0.8260 (mttp) cc_final: 0.8040 (mtpt) REVERT: D 338 GLU cc_start: 0.7039 (tt0) cc_final: 0.6788 (tt0) REVERT: D 370 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8034 (ttmt) REVERT: C 369 LYS cc_start: 0.7606 (mtpt) cc_final: 0.7176 (mttm) REVERT: E 369 LYS cc_start: 0.7506 (mtpt) cc_final: 0.7190 (mttp) REVERT: F 375 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7740 (tptm) REVERT: G 321 LYS cc_start: 0.7859 (mttt) cc_final: 0.7380 (tttt) REVERT: G 369 LYS cc_start: 0.7392 (mtpt) cc_final: 0.6980 (mttm) REVERT: H 315 LEU cc_start: 0.8049 (mt) cc_final: 0.7695 (mt) REVERT: H 369 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7729 (mtpp) REVERT: A 338 GLU cc_start: 0.5537 (mm-30) cc_final: 0.5116 (mm-30) REVERT: A 369 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7673 (mttp) outliers start: 16 outliers final: 7 residues processed: 113 average time/residue: 2.8526 time to fit residues: 334.4395 Evaluate side-chains 103 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.171433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.148667 restraints weight = 17303.205| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 1.89 r_work: 0.4195 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4105 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5283 Z= 0.260 Angle : 0.648 6.527 7065 Z= 0.350 Chirality : 0.051 0.141 792 Planarity : 0.005 0.043 900 Dihedral : 6.438 21.397 702 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.02 % Allowed : 17.85 % Favored : 80.13 % 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: -2.81 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 330 PHE 0.012 0.001 PHE B 378 TYR 0.011 0.002 TYR G 310 ARG 0.003 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8551 (mt) cc_final: 0.8243 (mm) REVERT: I 349 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6926 (mtp180) REVERT: I 369 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7878 (mtmm) REVERT: B 340 LYS cc_start: 0.7916 (tttm) cc_final: 0.7524 (ttmp) REVERT: B 351 GLN cc_start: 0.7965 (tt0) cc_final: 0.7662 (mt0) REVERT: D 321 LYS cc_start: 0.7784 (mttt) cc_final: 0.7516 (ttmm) REVERT: D 331 LYS cc_start: 0.8231 (mttp) cc_final: 0.8022 (mtpt) REVERT: D 338 GLU cc_start: 0.7091 (tt0) cc_final: 0.6846 (tt0) REVERT: D 370 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7953 (ttmt) REVERT: C 369 LYS cc_start: 0.7633 (mtpt) cc_final: 0.7174 (mttm) REVERT: E 369 LYS cc_start: 0.7494 (mtpt) cc_final: 0.7131 (mttp) REVERT: F 375 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7781 (tptm) REVERT: G 316 SER cc_start: 0.8280 (p) cc_final: 0.8022 (t) REVERT: G 321 LYS cc_start: 0.7859 (mttt) cc_final: 0.7402 (tttp) REVERT: G 349 ARG cc_start: 0.7628 (ttm110) cc_final: 0.7379 (ttp-110) REVERT: G 369 LYS cc_start: 0.7407 (mtpt) cc_final: 0.6967 (mttm) REVERT: H 315 LEU cc_start: 0.8079 (mt) cc_final: 0.7688 (mt) REVERT: H 369 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7777 (mtpp) REVERT: A 311 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8020 (mptp) REVERT: A 338 GLU cc_start: 0.5512 (mm-30) cc_final: 0.4732 (mm-30) REVERT: A 369 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7644 (mttp) outliers start: 12 outliers final: 7 residues processed: 112 average time/residue: 2.7822 time to fit residues: 323.6580 Evaluate side-chains 103 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain H residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.169945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.147039 restraints weight = 17396.971| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 1.90 r_work: 0.4180 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5283 Z= 0.288 Angle : 0.657 6.416 7065 Z= 0.354 Chirality : 0.051 0.136 792 Planarity : 0.005 0.047 900 Dihedral : 6.392 20.770 702 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.70 % Allowed : 16.84 % Favored : 79.46 % 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: -3.03 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 329 PHE 0.008 0.001 PHE B 378 TYR 0.011 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8550 (mt) cc_final: 0.8229 (mm) REVERT: I 349 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7031 (mtp180) REVERT: B 340 LYS cc_start: 0.7948 (tttm) cc_final: 0.7539 (ttmp) REVERT: B 342 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: B 349 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6802 (mtp180) REVERT: B 351 GLN cc_start: 0.7936 (tt0) cc_final: 0.7685 (mt0) REVERT: D 321 LYS cc_start: 0.7790 (mttt) cc_final: 0.7517 (ttmm) REVERT: D 331 LYS cc_start: 0.8232 (mttp) cc_final: 0.8029 (mtpt) REVERT: D 348 ASP cc_start: 0.7247 (t70) cc_final: 0.7010 (t70) REVERT: D 370 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8004 (ttmt) REVERT: C 369 LYS cc_start: 0.7678 (mtpt) cc_final: 0.7191 (mttm) REVERT: E 369 LYS cc_start: 0.7510 (mtpt) cc_final: 0.7162 (mttp) REVERT: E 379 ARG cc_start: 0.5285 (mtm180) cc_final: 0.4426 (pmt170) REVERT: F 311 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8257 (mtmm) REVERT: F 375 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7801 (tptm) REVERT: G 316 SER cc_start: 0.8291 (p) cc_final: 0.8081 (t) REVERT: G 321 LYS cc_start: 0.7862 (mttt) cc_final: 0.7427 (tttp) REVERT: G 369 LYS cc_start: 0.7391 (mtpt) cc_final: 0.6999 (mttm) REVERT: H 315 LEU cc_start: 0.8128 (mt) cc_final: 0.7728 (mt) REVERT: H 369 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7814 (mtpp) REVERT: A 311 LYS cc_start: 0.8357 (ttmt) cc_final: 0.8000 (mptp) REVERT: A 331 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7555 (tmtt) REVERT: A 369 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7616 (mttp) outliers start: 22 outliers final: 11 residues processed: 120 average time/residue: 2.9276 time to fit residues: 364.1261 Evaluate side-chains 118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 26 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.173225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.150294 restraints weight = 17208.562| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 1.90 r_work: 0.4214 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5283 Z= 0.167 Angle : 0.577 7.472 7065 Z= 0.308 Chirality : 0.050 0.130 792 Planarity : 0.005 0.047 900 Dihedral : 6.003 21.706 702 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.85 % Allowed : 18.18 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.91 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.005 0.001 PHE B 378 TYR 0.006 0.001 TYR G 310 ARG 0.009 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8563 (mt) cc_final: 0.8242 (mm) REVERT: I 349 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6935 (mtp180) REVERT: B 340 LYS cc_start: 0.7905 (tttm) cc_final: 0.7651 (tttt) REVERT: B 342 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: B 351 GLN cc_start: 0.7906 (tt0) cc_final: 0.7691 (mt0) REVERT: D 321 LYS cc_start: 0.7732 (mttt) cc_final: 0.7520 (ttmm) REVERT: C 369 LYS cc_start: 0.7695 (mtpt) cc_final: 0.7222 (mttm) REVERT: E 369 LYS cc_start: 0.7461 (mtpt) cc_final: 0.7103 (mttp) REVERT: E 379 ARG cc_start: 0.5252 (mtm180) cc_final: 0.4437 (pmt170) REVERT: F 375 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7758 (tptm) REVERT: G 321 LYS cc_start: 0.7813 (mttt) cc_final: 0.7355 (tptt) REVERT: G 369 LYS cc_start: 0.7367 (mtpt) cc_final: 0.6958 (mttm) REVERT: H 315 LEU cc_start: 0.8107 (mt) cc_final: 0.7682 (mt) REVERT: A 331 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7543 (tmtt) REVERT: A 369 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7564 (mttp) outliers start: 11 outliers final: 9 residues processed: 115 average time/residue: 2.8689 time to fit residues: 342.8467 Evaluate side-chains 111 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.173493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.150449 restraints weight = 17358.267| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 1.91 r_work: 0.4220 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5283 Z= 0.180 Angle : 0.573 7.025 7065 Z= 0.306 Chirality : 0.050 0.130 792 Planarity : 0.005 0.053 900 Dihedral : 5.803 21.931 702 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.85 % Allowed : 19.02 % Favored : 79.12 % 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: -2.90 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.009 0.001 PHE A 346 TYR 0.008 0.002 TYR G 310 ARG 0.010 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8579 (mt) cc_final: 0.8256 (mm) REVERT: I 336 GLN cc_start: 0.7371 (mt0) cc_final: 0.7124 (mt0) REVERT: I 349 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6931 (mtp180) REVERT: B 340 LYS cc_start: 0.7884 (tttm) cc_final: 0.7491 (ttmp) REVERT: B 342 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6587 (mt-10) REVERT: D 321 LYS cc_start: 0.7746 (mttt) cc_final: 0.7542 (ttmm) REVERT: C 369 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7239 (mttm) REVERT: E 369 LYS cc_start: 0.7458 (mtpt) cc_final: 0.7105 (mttp) REVERT: E 379 ARG cc_start: 0.5245 (mtm180) cc_final: 0.4431 (pmt170) REVERT: F 353 LYS cc_start: 0.7583 (ttpp) cc_final: 0.7209 (ttmm) REVERT: F 375 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7749 (tptm) REVERT: G 321 LYS cc_start: 0.7799 (mttt) cc_final: 0.7346 (tptt) REVERT: G 369 LYS cc_start: 0.7387 (mtpt) cc_final: 0.6980 (mttm) REVERT: H 315 LEU cc_start: 0.8102 (mt) cc_final: 0.7685 (mt) REVERT: A 331 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7536 (tmtt) REVERT: A 369 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7556 (mttp) outliers start: 11 outliers final: 8 residues processed: 114 average time/residue: 2.9995 time to fit residues: 354.3024 Evaluate side-chains 110 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.169421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.146473 restraints weight = 17355.037| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.88 r_work: 0.4169 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.4080 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5283 Z= 0.322 Angle : 0.672 7.180 7065 Z= 0.359 Chirality : 0.051 0.135 792 Planarity : 0.006 0.059 900 Dihedral : 6.244 22.031 702 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.53 % Allowed : 19.02 % Favored : 78.45 % 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: -3.07 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 329 PHE 0.008 0.002 PHE E 378 TYR 0.013 0.003 TYR A 310 ARG 0.012 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8561 (mt) cc_final: 0.8253 (mm) REVERT: I 336 GLN cc_start: 0.7412 (mt0) cc_final: 0.7148 (mt0) REVERT: I 349 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6949 (mtp180) REVERT: B 340 LYS cc_start: 0.7941 (tttm) cc_final: 0.7538 (ttmp) REVERT: B 342 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: D 321 LYS cc_start: 0.7781 (mttt) cc_final: 0.7545 (ttmm) REVERT: D 370 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8026 (ttmt) REVERT: C 369 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7224 (mttm) REVERT: E 369 LYS cc_start: 0.7536 (mtpt) cc_final: 0.7192 (mttp) REVERT: E 379 ARG cc_start: 0.5305 (mtm180) cc_final: 0.4488 (pmt170) REVERT: F 311 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8271 (mtmm) REVERT: F 353 LYS cc_start: 0.7604 (ttpp) cc_final: 0.7208 (ttmm) REVERT: F 375 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7807 (tptm) REVERT: F 379 ARG cc_start: 0.7404 (mpt180) cc_final: 0.7111 (mpt180) REVERT: G 321 LYS cc_start: 0.7808 (mttt) cc_final: 0.7393 (tttp) REVERT: G 369 LYS cc_start: 0.7401 (mtpt) cc_final: 0.7026 (mttm) REVERT: A 331 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7572 (tmtt) REVERT: A 369 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7604 (mttp) outliers start: 15 outliers final: 7 residues processed: 107 average time/residue: 3.1396 time to fit residues: 347.5023 Evaluate side-chains 108 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.173326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.150825 restraints weight = 17236.589| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 1.83 r_work: 0.4217 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5283 Z= 0.180 Angle : 0.590 7.729 7065 Z= 0.312 Chirality : 0.050 0.130 792 Planarity : 0.005 0.058 900 Dihedral : 5.906 22.217 702 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.02 % Allowed : 19.36 % Favored : 78.62 % 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: -2.98 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.007 0.001 PHE A 346 TYR 0.007 0.001 TYR G 310 ARG 0.011 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8573 (mt) cc_final: 0.8262 (mm) REVERT: I 336 GLN cc_start: 0.7415 (mt0) cc_final: 0.7173 (mt0) REVERT: I 349 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6959 (mtp180) REVERT: I 369 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7973 (mttt) REVERT: B 342 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6613 (mt-10) REVERT: C 369 LYS cc_start: 0.7709 (mtpt) cc_final: 0.7226 (mttm) REVERT: E 369 LYS cc_start: 0.7460 (mtpt) cc_final: 0.7119 (mttp) REVERT: E 379 ARG cc_start: 0.5284 (mtm180) cc_final: 0.4457 (pmt170) REVERT: F 311 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8209 (mtmm) REVERT: F 375 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7772 (tptm) REVERT: F 379 ARG cc_start: 0.7327 (mpt180) cc_final: 0.7051 (mpt180) REVERT: G 321 LYS cc_start: 0.7783 (mttt) cc_final: 0.7372 (tptt) REVERT: G 369 LYS cc_start: 0.7366 (mtpt) cc_final: 0.6966 (mttm) REVERT: A 331 LYS cc_start: 0.8343 (mtpt) cc_final: 0.7565 (tmtt) REVERT: A 369 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7527 (mttp) outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 3.0358 time to fit residues: 349.1085 Evaluate side-chains 114 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.167194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.144356 restraints weight = 17756.727| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 1.88 r_work: 0.4142 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.4053 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5283 Z= 0.422 Angle : 0.749 7.371 7065 Z= 0.399 Chirality : 0.053 0.137 792 Planarity : 0.006 0.064 900 Dihedral : 6.487 23.478 702 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.85 % Allowed : 19.70 % Favored : 78.45 % 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: -3.23 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 329 PHE 0.009 0.002 PHE E 378 TYR 0.016 0.003 TYR A 310 ARG 0.011 0.001 ARG G 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.922 Fit side-chains REVERT: I 308 ILE cc_start: 0.8573 (mt) cc_final: 0.8270 (mm) REVERT: I 336 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7159 (mt0) REVERT: I 349 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6921 (mtp180) REVERT: B 340 LYS cc_start: 0.7947 (tttm) cc_final: 0.7737 (ttmm) REVERT: C 369 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7226 (mttm) REVERT: E 369 LYS cc_start: 0.7580 (mtpt) cc_final: 0.7235 (mttp) REVERT: E 379 ARG cc_start: 0.5345 (mtm180) cc_final: 0.4291 (ptp90) REVERT: F 311 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8311 (mtmm) REVERT: F 375 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7847 (tptm) REVERT: F 379 ARG cc_start: 0.7383 (mpt180) cc_final: 0.7080 (mpt180) REVERT: G 321 LYS cc_start: 0.7821 (mttt) cc_final: 0.7398 (tttp) REVERT: G 369 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7034 (mttm) REVERT: A 331 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7584 (tmtt) REVERT: A 369 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7637 (mttp) outliers start: 11 outliers final: 7 residues processed: 103 average time/residue: 3.0525 time to fit residues: 325.4628 Evaluate side-chains 105 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 349 ARG Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.170563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.147784 restraints weight = 17344.279| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.90 r_work: 0.4186 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4096 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5283 Z= 0.210 Angle : 0.628 7.916 7065 Z= 0.332 Chirality : 0.050 0.131 792 Planarity : 0.005 0.063 900 Dihedral : 6.131 23.379 702 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.52 % Allowed : 20.37 % Favored : 78.11 % 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: -3.10 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.007 0.001 PHE B 378 TYR 0.008 0.002 TYR G 310 ARG 0.012 0.001 ARG G 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9583.71 seconds wall clock time: 169 minutes 25.01 seconds (10165.01 seconds total)