Starting phenix.real_space_refine on Mon Jul 28 17:42:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8s_18259/07_2025/8q8s_18259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8s_18259/07_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_18259/07_2025/8q8s_18259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8s_18259/07_2025/8q8s_18259.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8s_18259/07_2025/8q8s_18259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8s_18259/07_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.40, per 1000 atoms: 0.70 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: 2.64 Conformation dependent library (CDL) restraints added in 694.7 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: 1.59 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: 4.05 Time building geometry restraints manager: 3.21 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 170.560 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: 0.190 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.490 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:15.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.210 ------------------------------------------------------------------------------- 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= 0.712 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 Details of bonding type rmsd hydrogen bonds : bond 0.11238 ( 85) hydrogen bonds : angle 7.47572 ( 255) covalent geometry : bond 0.01149 ( 5283) covalent geometry : angle 2.11358 ( 7065) *********************** 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 : 1.003 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: 3.1888 time to fit residues: 658.4521 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 : 0.830 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.154082 restraints weight = 17895.448| |-----------------------------------------------------------------------------| 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: 0.4158 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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= 0.207 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 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 85) hydrogen bonds : angle 5.50137 ( 255) covalent geometry : bond 0.00447 ( 5283) covalent geometry : angle 0.74252 ( 7065) *********************** 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 : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8533 (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: 0.7693 (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: 0.8181 (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: 0.7446 (OUTLIER) cc_final: 0.7077 (mtp180) REVERT: B 351 GLN cc_start: 0.8051 (tt0) cc_final: 0.7708 (mt0) REVERT: D 321 LYS cc_start: 0.7759 (mttt) cc_final: 0.7465 (ttmm) REVERT: D 338 GLU cc_start: 0.7029 (tt0) cc_final: 0.6788 (tt0) REVERT: C 353 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7481 (mmtt) REVERT: C 369 LYS cc_start: 0.7538 (mtpt) cc_final: 0.7140 (mttm) REVERT: E 369 LYS cc_start: 0.7513 (mtpt) cc_final: 0.7199 (mttp) REVERT: F 375 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7789 (tptt) REVERT: G 321 LYS cc_start: 0.7890 (mttt) cc_final: 0.7383 (tttt) REVERT: G 369 LYS cc_start: 0.7420 (mtpt) cc_final: 0.7039 (mttm) REVERT: H 315 LEU cc_start: 0.8032 (mt) cc_final: 0.7698 (mt) REVERT: H 344 LEU cc_start: 0.7172 (mt) cc_final: 0.6895 (mt) REVERT: H 345 ASP cc_start: 0.6378 (t0) cc_final: 0.6063 (m-30) REVERT: H 353 LYS cc_start: 0.7369 (mtpp) cc_final: 0.7055 (ttpp) REVERT: H 369 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7689 (mtpp) REVERT: A 338 GLU cc_start: 0.5456 (mm-30) cc_final: 0.5170 (mm-30) REVERT: A 369 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7646 (mttp) outliers start: 15 outliers final: 4 residues processed: 129 average time/residue: 3.1980 time to fit residues: 430.9308 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 : 0.969 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4536 r_free = 0.4536 target = 0.175055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.152328 restraints weight = 17355.782| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 1.91 r_work: 0.4233 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5283 Z= 0.138 Angle : 0.620 6.779 7065 Z= 0.337 Chirality : 0.051 0.144 792 Planarity : 0.004 0.039 900 Dihedral : 6.389 22.003 702 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.36 % Allowed : 16.50 % 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: -2.41 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 330 PHE 0.006 0.001 PHE A 346 TYR 0.011 0.002 TYR D 310 ARG 0.004 0.001 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02494 ( 85) hydrogen bonds : angle 4.95161 ( 255) covalent geometry : bond 0.00284 ( 5283) covalent geometry : angle 0.62015 ( 7065) *********************** 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 118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8541 (mt) cc_final: 0.8219 (mm) REVERT: I 317 LYS cc_start: 0.7726 (pttt) cc_final: 0.7410 (ptpt) REVERT: I 349 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6952 (mtp180) REVERT: I 369 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7877 (mtmm) REVERT: B 340 LYS cc_start: 0.7875 (tttm) cc_final: 0.7482 (ttmp) REVERT: B 351 GLN cc_start: 0.7969 (tt0) cc_final: 0.7662 (mt0) REVERT: D 321 LYS cc_start: 0.7768 (mttt) cc_final: 0.7488 (ttmm) REVERT: D 331 LYS cc_start: 0.8251 (mttp) cc_final: 0.8035 (mtpt) REVERT: D 338 GLU cc_start: 0.7025 (tt0) cc_final: 0.6786 (tt0) REVERT: D 370 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8015 (ttmt) REVERT: C 369 LYS cc_start: 0.7602 (mtpt) cc_final: 0.7172 (mttm) REVERT: E 369 LYS cc_start: 0.7484 (mtpt) cc_final: 0.7166 (mttp) REVERT: G 321 LYS cc_start: 0.7808 (mttt) cc_final: 0.7344 (tttt) REVERT: G 369 LYS cc_start: 0.7370 (mtpt) cc_final: 0.6969 (mttm) REVERT: H 315 LEU cc_start: 0.8059 (mt) cc_final: 0.7699 (mt) REVERT: H 369 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7706 (mtpp) REVERT: A 338 GLU cc_start: 0.5481 (mm-30) cc_final: 0.5048 (mm-30) REVERT: A 369 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7665 (mttp) outliers start: 14 outliers final: 6 residues processed: 116 average time/residue: 2.9371 time to fit residues: 354.1457 Evaluate side-chains 102 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 = 0.171522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.148647 restraints weight = 17362.272| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 1.88 r_work: 0.4198 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.4108 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5283 Z= 0.181 Angle : 0.653 6.500 7065 Z= 0.353 Chirality : 0.051 0.134 792 Planarity : 0.005 0.044 900 Dihedral : 6.426 21.261 702 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.53 % Allowed : 17.17 % Favored : 80.30 % 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: -2.73 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 330 PHE 0.013 0.001 PHE B 378 TYR 0.011 0.002 TYR A 310 ARG 0.002 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02582 ( 85) hydrogen bonds : angle 4.97244 ( 255) covalent geometry : bond 0.00388 ( 5283) covalent geometry : angle 0.65294 ( 7065) *********************** 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 117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8577 (mt) cc_final: 0.8258 (mm) REVERT: I 317 LYS cc_start: 0.7778 (pttt) cc_final: 0.7404 (ptpt) REVERT: I 349 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6898 (mtp180) REVERT: I 369 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7869 (mtmm) REVERT: B 340 LYS cc_start: 0.7920 (tttm) cc_final: 0.7525 (ttmp) REVERT: B 351 GLN cc_start: 0.7994 (tt0) cc_final: 0.7692 (mt0) REVERT: D 311 LYS cc_start: 0.8053 (tptp) cc_final: 0.7827 (ttpt) REVERT: D 321 LYS cc_start: 0.7779 (mttt) cc_final: 0.7516 (ttmm) REVERT: D 331 LYS cc_start: 0.8239 (mttp) cc_final: 0.8029 (mtpt) REVERT: D 338 GLU cc_start: 0.7106 (tt0) cc_final: 0.6851 (tt0) REVERT: D 370 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7998 (ttmt) REVERT: C 369 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7167 (mttm) REVERT: E 369 LYS cc_start: 0.7491 (mtpt) cc_final: 0.7124 (mttp) REVERT: F 375 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7772 (tptm) REVERT: G 316 SER cc_start: 0.8242 (p) cc_final: 0.7982 (t) REVERT: G 321 LYS cc_start: 0.7864 (mttt) cc_final: 0.7404 (tttp) REVERT: G 349 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7391 (ttp-110) REVERT: G 369 LYS cc_start: 0.7402 (mtpt) cc_final: 0.7002 (mttm) REVERT: H 315 LEU cc_start: 0.8080 (mt) cc_final: 0.7704 (mt) REVERT: H 369 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7780 (mtpp) REVERT: A 338 GLU cc_start: 0.5528 (mm-30) cc_final: 0.5011 (mm-30) REVERT: A 369 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7644 (mttp) outliers start: 15 outliers final: 8 residues processed: 113 average time/residue: 3.6078 time to fit residues: 424.6731 Evaluate side-chains 104 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 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: 0.3980 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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 = 0.4510 r_free = 0.4510 target = 0.171975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.148823 restraints weight = 17275.648| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 1.91 r_work: 0.4193 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5283 Z= 0.164 Angle : 0.625 6.519 7065 Z= 0.337 Chirality : 0.050 0.135 792 Planarity : 0.005 0.047 900 Dihedral : 6.235 20.536 702 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.69 % Allowed : 17.17 % 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: -2.90 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.008 0.001 PHE B 378 TYR 0.010 0.002 TYR D 310 ARG 0.003 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02449 ( 85) hydrogen bonds : angle 4.89622 ( 255) covalent geometry : bond 0.00348 ( 5283) covalent geometry : angle 0.62485 ( 7065) *********************** 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 118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8564 (mt) cc_final: 0.8240 (mm) REVERT: I 349 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6913 (mtp180) REVERT: I 369 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7899 (mtmm) REVERT: B 340 LYS cc_start: 0.7914 (tttm) cc_final: 0.7506 (ttmp) REVERT: B 342 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6723 (mt-10) REVERT: B 351 GLN cc_start: 0.7941 (tt0) cc_final: 0.7680 (mt0) REVERT: D 311 LYS cc_start: 0.8056 (tptp) cc_final: 0.7812 (ttpt) REVERT: D 321 LYS cc_start: 0.7784 (mttt) cc_final: 0.7517 (ttmm) REVERT: D 331 LYS cc_start: 0.8225 (mttp) cc_final: 0.8019 (mtpt) REVERT: D 370 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7982 (ttmt) REVERT: C 369 LYS cc_start: 0.7677 (mtpt) cc_final: 0.7202 (mttm) REVERT: E 369 LYS cc_start: 0.7487 (mtpt) cc_final: 0.7127 (mttp) REVERT: E 379 ARG cc_start: 0.5350 (mtm180) cc_final: 0.4491 (pmt170) REVERT: F 353 LYS cc_start: 0.7523 (ttpp) cc_final: 0.7193 (ttmm) REVERT: F 375 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7787 (tptm) REVERT: G 316 SER cc_start: 0.8250 (p) cc_final: 0.8029 (t) REVERT: G 321 LYS cc_start: 0.7876 (mttt) cc_final: 0.7412 (tttp) REVERT: G 369 LYS cc_start: 0.7386 (mtpt) cc_final: 0.6951 (mttm) REVERT: H 315 LEU cc_start: 0.8126 (mt) cc_final: 0.7722 (mt) REVERT: A 338 GLU cc_start: 0.5511 (mm-30) cc_final: 0.5066 (mm-30) REVERT: A 369 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7642 (mttp) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 3.2130 time to fit residues: 370.4376 Evaluate side-chains 111 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4520 r_free = 0.4520 target = 0.172883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.150002 restraints weight = 17281.926| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 1.86 r_work: 0.4207 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.4120 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5283 Z= 0.134 Angle : 0.588 6.663 7065 Z= 0.314 Chirality : 0.050 0.131 792 Planarity : 0.005 0.051 900 Dihedral : 5.951 22.038 702 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.69 % Allowed : 17.68 % Favored : 79.63 % 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 0.004 0.001 HIS B 330 PHE 0.005 0.001 PHE B 378 TYR 0.009 0.002 TYR D 310 ARG 0.006 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02158 ( 85) hydrogen bonds : angle 4.75320 ( 255) covalent geometry : bond 0.00286 ( 5283) covalent geometry : angle 0.58755 ( 7065) *********************** 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 121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8588 (mt) cc_final: 0.8262 (mm) REVERT: I 336 GLN cc_start: 0.7414 (mt0) cc_final: 0.7201 (mt0) REVERT: I 349 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6776 (mtp180) REVERT: I 369 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7903 (mtmm) REVERT: B 342 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6603 (mt-10) REVERT: B 351 GLN cc_start: 0.7921 (tt0) cc_final: 0.7693 (mt0) REVERT: D 311 LYS cc_start: 0.8018 (tptp) cc_final: 0.7751 (ttpt) REVERT: D 370 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7940 (ttmt) REVERT: C 369 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7223 (mttm) REVERT: E 369 LYS cc_start: 0.7458 (mtpt) cc_final: 0.7106 (mttp) REVERT: E 379 ARG cc_start: 0.5374 (mtm180) cc_final: 0.4550 (pmt170) REVERT: F 353 LYS cc_start: 0.7560 (ttpp) cc_final: 0.7203 (ttmm) REVERT: F 375 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7778 (tptm) REVERT: G 316 SER cc_start: 0.8266 (p) cc_final: 0.8042 (t) REVERT: G 321 LYS cc_start: 0.7845 (mttt) cc_final: 0.7381 (tptt) REVERT: G 369 LYS cc_start: 0.7375 (mtpt) cc_final: 0.6998 (mttm) REVERT: H 315 LEU cc_start: 0.8104 (mt) cc_final: 0.7700 (mt) REVERT: A 331 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7551 (tmtt) REVERT: A 338 GLU cc_start: 0.5539 (mm-30) cc_final: 0.5046 (mm-30) REVERT: A 369 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7566 (mttp) outliers start: 16 outliers final: 8 residues processed: 116 average time/residue: 2.8062 time to fit residues: 337.5180 Evaluate side-chains 112 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain H residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.4510 r_free = 0.4510 target = 0.171671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.148645 restraints weight = 17467.589| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 1.87 r_work: 0.4196 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.4109 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5283 Z= 0.154 Angle : 0.602 6.787 7065 Z= 0.322 Chirality : 0.050 0.134 792 Planarity : 0.005 0.055 900 Dihedral : 5.959 23.009 702 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.86 % Allowed : 18.18 % Favored : 78.96 % 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: -2.97 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.009 0.001 PHE A 346 TYR 0.009 0.002 TYR D 310 ARG 0.010 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02302 ( 85) hydrogen bonds : angle 4.73597 ( 255) covalent geometry : bond 0.00328 ( 5283) covalent geometry : angle 0.60198 ( 7065) *********************** 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 121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8568 (mt) cc_final: 0.8243 (mm) REVERT: I 336 GLN cc_start: 0.7417 (mt0) cc_final: 0.7184 (mt0) REVERT: I 349 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6857 (mtp180) REVERT: B 340 LYS cc_start: 0.7885 (tttm) cc_final: 0.7539 (ttmp) REVERT: B 342 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: D 370 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7972 (ttmt) REVERT: C 369 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7220 (mttm) REVERT: E 369 LYS cc_start: 0.7479 (mtpt) cc_final: 0.7129 (mttp) REVERT: E 379 ARG cc_start: 0.5277 (mtm180) cc_final: 0.4442 (pmt170) REVERT: F 311 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8227 (mtmm) REVERT: F 353 LYS cc_start: 0.7566 (ttpp) cc_final: 0.7166 (ttmm) REVERT: F 375 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7785 (tptm) REVERT: G 316 SER cc_start: 0.8232 (p) cc_final: 0.8025 (t) REVERT: G 321 LYS cc_start: 0.7820 (mttt) cc_final: 0.7351 (tptt) REVERT: G 369 LYS cc_start: 0.7381 (mtpt) cc_final: 0.7001 (mttm) REVERT: H 315 LEU cc_start: 0.8115 (mt) cc_final: 0.7710 (mt) REVERT: A 331 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7547 (tmtt) REVERT: A 338 GLU cc_start: 0.5490 (mm-30) cc_final: 0.4870 (mm-30) REVERT: A 369 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7559 (mttp) outliers start: 17 outliers final: 8 residues processed: 116 average time/residue: 2.8261 time to fit residues: 339.6355 Evaluate side-chains 113 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 chunk 57 optimal weight: 4.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.170673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.147802 restraints weight = 17246.402| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 1.88 r_work: 0.4184 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.4096 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5283 Z= 0.170 Angle : 0.618 6.810 7065 Z= 0.330 Chirality : 0.050 0.133 792 Planarity : 0.005 0.052 900 Dihedral : 6.036 22.803 702 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: -3.05 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 329 PHE 0.006 0.001 PHE B 378 TYR 0.010 0.002 TYR A 310 ARG 0.011 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02407 ( 85) hydrogen bonds : angle 4.76835 ( 255) covalent geometry : bond 0.00367 ( 5283) covalent geometry : angle 0.61830 ( 7065) *********************** 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 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.885 Fit side-chains REVERT: I 308 ILE cc_start: 0.8583 (mt) cc_final: 0.8257 (mm) REVERT: I 349 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6823 (mtp180) REVERT: B 340 LYS cc_start: 0.7891 (tttm) cc_final: 0.7676 (ttmm) REVERT: B 342 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: B 349 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6819 (mtp180) REVERT: D 370 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7989 (ttmt) REVERT: C 369 LYS cc_start: 0.7711 (mtpt) cc_final: 0.7218 (mttm) REVERT: E 369 LYS cc_start: 0.7480 (mtpt) cc_final: 0.7135 (mttp) REVERT: E 379 ARG cc_start: 0.5277 (mtm180) cc_final: 0.4444 (pmt170) REVERT: F 311 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8245 (mtmm) REVERT: F 375 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7816 (tptm) REVERT: G 316 SER cc_start: 0.8251 (p) cc_final: 0.7885 (t) REVERT: G 321 LYS cc_start: 0.7806 (mttt) cc_final: 0.7386 (tttp) REVERT: G 369 LYS cc_start: 0.7380 (mtpt) cc_final: 0.6981 (mttm) REVERT: A 331 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7558 (tmtt) REVERT: A 338 GLU cc_start: 0.5449 (mm-30) cc_final: 0.4936 (mm-30) REVERT: A 369 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7551 (mttp) outliers start: 15 outliers final: 9 residues processed: 113 average time/residue: 2.9169 time to fit residues: 342.4199 Evaluate side-chains 112 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 F residue 320 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain H residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 0.0270 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 overall best weight: 2.7442 ------------------------------------------------------------------------------- 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** B 336 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.171600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.148979 restraints weight = 17365.089| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 1.87 r_work: 0.4205 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4115 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5283 Z= 0.143 Angle : 0.601 7.725 7065 Z= 0.319 Chirality : 0.050 0.131 792 Planarity : 0.005 0.048 900 Dihedral : 5.892 22.666 702 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.19 % Allowed : 19.70 % 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: -3.04 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (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 A 310 ARG 0.012 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02220 ( 85) hydrogen bonds : angle 4.69485 ( 255) covalent geometry : bond 0.00307 ( 5283) covalent geometry : angle 0.60089 ( 7065) *********************** 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 109 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.892 Fit side-chains REVERT: I 308 ILE cc_start: 0.8574 (mt) cc_final: 0.8264 (mm) REVERT: I 349 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6796 (mtp180) REVERT: I 369 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7901 (mtmm) REVERT: B 340 LYS cc_start: 0.7872 (tttm) cc_final: 0.7652 (ttmm) REVERT: B 342 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6702 (mt-10) REVERT: D 370 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7959 (ttmt) REVERT: C 369 LYS cc_start: 0.7709 (mtpt) cc_final: 0.7203 (mttm) REVERT: E 369 LYS cc_start: 0.7461 (mtpt) cc_final: 0.7112 (mttp) REVERT: E 379 ARG cc_start: 0.5278 (mtm180) cc_final: 0.4443 (pmt170) REVERT: F 311 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8236 (mtmm) REVERT: F 375 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7807 (tptm) REVERT: G 316 SER cc_start: 0.8238 (p) cc_final: 0.7882 (t) REVERT: G 321 LYS cc_start: 0.7805 (mttt) cc_final: 0.7354 (tptt) REVERT: G 369 LYS cc_start: 0.7368 (mtpt) cc_final: 0.6953 (mttm) REVERT: A 331 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7552 (tmtt) REVERT: A 338 GLU cc_start: 0.5549 (mm-30) cc_final: 0.4984 (mm-30) REVERT: A 369 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7547 (mttp) outliers start: 13 outliers final: 8 residues processed: 105 average time/residue: 2.8696 time to fit residues: 312.4511 Evaluate side-chains 111 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 F residue 324 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 53 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.171212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.148498 restraints weight = 17459.337| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 1.87 r_work: 0.4191 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4103 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5283 Z= 0.152 Angle : 0.614 7.631 7065 Z= 0.324 Chirality : 0.050 0.131 792 Planarity : 0.005 0.057 900 Dihedral : 5.887 22.582 702 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.19 % Allowed : 19.70 % 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: -3.07 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (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 0.009 0.002 TYR A 310 ARG 0.013 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02251 ( 85) hydrogen bonds : angle 4.73660 ( 255) covalent geometry : bond 0.00329 ( 5283) covalent geometry : angle 0.61399 ( 7065) ********************** 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 110 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.800 Fit side-chains REVERT: I 308 ILE cc_start: 0.8584 (mt) cc_final: 0.8271 (mm) REVERT: I 311 LYS cc_start: 0.7888 (tmtm) cc_final: 0.7643 (tmmm) REVERT: I 349 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6768 (mtp180) REVERT: I 369 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7899 (mtmm) REVERT: B 340 LYS cc_start: 0.7901 (tttm) cc_final: 0.7676 (ttmm) REVERT: B 342 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: D 370 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7990 (ttmt) REVERT: C 369 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7189 (mttm) REVERT: E 369 LYS cc_start: 0.7479 (mtpt) cc_final: 0.7124 (mttp) REVERT: E 379 ARG cc_start: 0.5288 (mtm180) cc_final: 0.4453 (pmt170) REVERT: F 311 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8248 (mtmm) REVERT: F 375 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7834 (tptm) REVERT: G 316 SER cc_start: 0.8244 (p) cc_final: 0.7894 (t) REVERT: G 321 LYS cc_start: 0.7795 (mttt) cc_final: 0.7358 (tptt) REVERT: G 369 LYS cc_start: 0.7375 (mtpt) cc_final: 0.6958 (mttm) REVERT: A 331 LYS cc_start: 0.8364 (mtpt) cc_final: 0.7557 (tmtt) REVERT: A 338 GLU cc_start: 0.5557 (mm-30) cc_final: 0.4996 (mm-30) REVERT: A 369 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7554 (mttp) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 2.8472 time to fit residues: 318.7870 Evaluate side-chains 109 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 F residue 324 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain H residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.0070 chunk 56 optimal weight: 0.0670 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.7940 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.173745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.151063 restraints weight = 17117.096| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 1.87 r_work: 0.4220 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5283 Z= 0.115 Angle : 0.573 8.052 7065 Z= 0.302 Chirality : 0.050 0.127 792 Planarity : 0.005 0.059 900 Dihedral : 5.635 21.613 702 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.02 % Allowed : 19.70 % Favored : 78.28 % 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: -2.99 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.009 0.001 PHE A 346 TYR 0.007 0.001 TYR G 310 ARG 0.013 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01916 ( 85) hydrogen bonds : angle 4.59584 ( 255) covalent geometry : bond 0.00254 ( 5283) covalent geometry : angle 0.57291 ( 7065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11025.89 seconds wall clock time: 195 minutes 22.54 seconds (11722.54 seconds total)