Starting phenix.real_space_refine on Sat Aug 23 07:30:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8s_18259/08_2025/8q8s_18259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8s_18259/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q8s_18259/08_2025/8q8s_18259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8s_18259/08_2025/8q8s_18259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q8s_18259/08_2025/8q8s_18259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8s_18259/08_2025/8q8s_18259.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.30, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 256.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.30 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: 2.21 Time building geometry restraints manager: 1.40 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: 0.00 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: 4.330 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: 0.080 Extract box with map and model: 0.360 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.890 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (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 ARG 0.006 0.001 ARG G 379 TYR 0.077 0.023 TYR D 310 PHE 0.056 0.012 PHE F 378 HIS 0.018 0.005 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.01149 ( 5283) covalent geometry : angle 2.11358 ( 7065) hydrogen bonds : bond 0.11238 ( 85) hydrogen bonds : angle 7.47572 ( 255) *********************** 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 : 0.301 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: 0.7614 (mtmm) REVERT: I 375 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7477 (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: 0.6255 (tt0) REVERT: D 358 ASP cc_start: 0.7678 (m-30) cc_final: 0.7436 (m-30) REVERT: C 353 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7254 (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: 0.7558 (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: 0.7443 (mttt) REVERT: G 369 LYS cc_start: 0.7054 (mtpt) cc_final: 0.6728 (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: 0.6330 (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: 0.7439 (tmtt) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 1.4799 time to fit residues: 303.9978 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 : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS F 307 GLN F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.181450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.158685 restraints weight = 16814.476| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 1.86 r_work: 0.4283 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4195 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5283 Z= 0.153 Angle : 0.699 6.673 7065 Z= 0.380 Chirality : 0.049 0.139 792 Planarity : 0.004 0.032 900 Dihedral : 6.888 27.846 702 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.19 % Allowed : 14.81 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 349 TYR 0.007 0.002 TYR G 310 PHE 0.005 0.001 PHE A 346 HIS 0.005 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5283) covalent geometry : angle 0.69927 ( 7065) hydrogen bonds : bond 0.02919 ( 85) hydrogen bonds : angle 5.46711 ( 255) *********************** 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: 13 poor density : 123 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8540 (mt) cc_final: 0.8214 (mm) REVERT: I 317 LYS cc_start: 0.7760 (pttt) cc_final: 0.7428 (ptpt) REVERT: I 349 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7144 (mtp180) REVERT: I 369 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7873 (mtmm) REVERT: B 311 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7931 (tmmt) REVERT: B 340 LYS cc_start: 0.7838 (tttm) cc_final: 0.7462 (ttmp) REVERT: B 349 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7129 (mtp180) REVERT: B 351 GLN cc_start: 0.8022 (tt0) cc_final: 0.7679 (mt0) REVERT: D 321 LYS cc_start: 0.7707 (mttt) cc_final: 0.7428 (ttmm) REVERT: D 338 GLU cc_start: 0.6974 (tt0) cc_final: 0.6732 (tt0) REVERT: C 353 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7458 (mmtt) REVERT: C 369 LYS cc_start: 0.7519 (mtpt) cc_final: 0.7137 (mttm) REVERT: E 369 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7136 (mttp) REVERT: F 375 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7729 (tttt) REVERT: G 321 LYS cc_start: 0.7851 (mttt) cc_final: 0.7297 (tptt) REVERT: G 369 LYS cc_start: 0.7339 (mtpt) cc_final: 0.6969 (mttm) REVERT: H 315 LEU cc_start: 0.8003 (mt) cc_final: 0.7640 (mt) REVERT: H 344 LEU cc_start: 0.7134 (mt) cc_final: 0.6840 (mt) REVERT: H 345 ASP cc_start: 0.6318 (t0) cc_final: 0.6056 (m-30) REVERT: H 369 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7598 (mtpp) REVERT: A 338 GLU cc_start: 0.5419 (mm-30) cc_final: 0.5101 (mm-30) REVERT: A 369 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7635 (mttp) outliers start: 13 outliers final: 5 residues processed: 129 average time/residue: 1.4603 time to fit residues: 194.8210 Evaluate side-chains 105 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 F residue 316 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 2 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.0060 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN D 351 GLN G 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.171949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.149180 restraints weight = 17606.700| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 1.89 r_work: 0.4205 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4115 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5283 Z= 0.200 Angle : 0.698 6.553 7065 Z= 0.380 Chirality : 0.052 0.152 792 Planarity : 0.005 0.047 900 Dihedral : 6.671 22.440 702 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.37 % Allowed : 15.32 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 349 TYR 0.014 0.003 TYR D 310 PHE 0.010 0.002 PHE D 378 HIS 0.009 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 5283) covalent geometry : angle 0.69806 ( 7065) hydrogen bonds : bond 0.02819 ( 85) hydrogen bonds : angle 5.21926 ( 255) *********************** 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 122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8554 (mt) cc_final: 0.8236 (mm) REVERT: I 317 LYS cc_start: 0.7764 (pttt) cc_final: 0.7455 (ptpt) REVERT: I 349 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6959 (mtp180) REVERT: I 369 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7890 (mtmm) REVERT: B 340 LYS cc_start: 0.7912 (tttm) cc_final: 0.7525 (ttmp) REVERT: B 342 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6849 (mt-10) REVERT: B 349 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7057 (mtp180) REVERT: B 351 GLN cc_start: 0.7977 (tt0) cc_final: 0.7659 (mt0) REVERT: D 321 LYS cc_start: 0.7778 (mttt) cc_final: 0.7492 (ttmm) REVERT: D 338 GLU cc_start: 0.7059 (tt0) cc_final: 0.6825 (tt0) REVERT: D 370 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8041 (ttmt) REVERT: C 369 LYS cc_start: 0.7593 (mtpt) cc_final: 0.7168 (mttm) REVERT: E 369 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7194 (mttp) REVERT: F 375 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7759 (tptm) REVERT: G 321 LYS cc_start: 0.7890 (mttt) cc_final: 0.7373 (tptt) REVERT: G 347 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7493 (mtpp) REVERT: G 369 LYS cc_start: 0.7391 (mtpt) cc_final: 0.6985 (mttm) REVERT: H 315 LEU cc_start: 0.8085 (mt) cc_final: 0.7741 (mt) REVERT: A 338 GLU cc_start: 0.5553 (mm-30) cc_final: 0.5069 (mm-30) REVERT: A 369 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7675 (mttp) outliers start: 20 outliers final: 8 residues processed: 118 average time/residue: 1.5855 time to fit residues: 193.2024 Evaluate side-chains 103 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 343 LYS Chi-restraints excluded: chain C residue 375 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 Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.174826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.152064 restraints weight = 17367.338| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 1.87 r_work: 0.4239 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.4149 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5283 Z= 0.122 Angle : 0.587 6.722 7065 Z= 0.317 Chirality : 0.050 0.132 792 Planarity : 0.005 0.078 900 Dihedral : 6.185 21.189 702 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.85 % Allowed : 17.34 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 349 TYR 0.008 0.001 TYR G 310 PHE 0.007 0.001 PHE D 378 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 5283) covalent geometry : angle 0.58700 ( 7065) hydrogen bonds : bond 0.02143 ( 85) hydrogen bonds : angle 4.87219 ( 255) *********************** 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 113 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8556 (mt) cc_final: 0.8230 (mm) REVERT: I 317 LYS cc_start: 0.7754 (pttt) cc_final: 0.7438 (ptpt) REVERT: I 349 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6862 (mtp180) REVERT: I 369 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7877 (mtmm) REVERT: B 340 LYS cc_start: 0.7841 (tttm) cc_final: 0.7464 (ttmp) REVERT: B 351 GLN cc_start: 0.7953 (tt0) cc_final: 0.7665 (mt0) REVERT: D 321 LYS cc_start: 0.7750 (mttt) cc_final: 0.7496 (ttmm) REVERT: D 331 LYS cc_start: 0.8247 (mttp) cc_final: 0.8004 (mtpt) REVERT: D 338 GLU cc_start: 0.7072 (tt0) cc_final: 0.6798 (tt0) REVERT: D 370 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7964 (ttmt) REVERT: C 369 LYS cc_start: 0.7635 (mtpt) cc_final: 0.7178 (mttm) REVERT: E 369 LYS cc_start: 0.7476 (mtpt) cc_final: 0.7146 (mttp) REVERT: G 316 SER cc_start: 0.8229 (p) cc_final: 0.7920 (t) REVERT: G 321 LYS cc_start: 0.7822 (mttt) cc_final: 0.7342 (tptt) REVERT: G 369 LYS cc_start: 0.7370 (mtpt) cc_final: 0.6969 (mttm) REVERT: H 315 LEU cc_start: 0.8061 (mt) cc_final: 0.7674 (mt) REVERT: A 338 GLU cc_start: 0.5518 (mm-30) cc_final: 0.4966 (mm-30) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 1.3429 time to fit residues: 152.8610 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 : 0.320 ------------------------------------------------------------------------------- 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 C residue 375 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 343 LYS 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 23 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4506 r_free = 0.4506 target = 0.171486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.148374 restraints weight = 17332.383| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 1.90 r_work: 0.4196 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5283 Z= 0.182 Angle : 0.635 6.530 7065 Z= 0.343 Chirality : 0.051 0.136 792 Planarity : 0.005 0.054 900 Dihedral : 6.221 20.438 702 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.19 % Allowed : 18.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 349 TYR 0.012 0.003 TYR G 310 PHE 0.007 0.001 PHE D 378 HIS 0.006 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5283) covalent geometry : angle 0.63538 ( 7065) hydrogen bonds : bond 0.02488 ( 85) hydrogen bonds : angle 4.99373 ( 255) *********************** 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 111 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8560 (mt) cc_final: 0.8248 (mm) REVERT: I 349 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6853 (mtp180) REVERT: I 369 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7888 (mtmm) REVERT: B 340 LYS cc_start: 0.7888 (tttm) cc_final: 0.7499 (ttmp) REVERT: B 351 GLN cc_start: 0.7952 (tt0) cc_final: 0.7685 (mt0) REVERT: D 321 LYS cc_start: 0.7793 (mttt) cc_final: 0.7517 (ttmm) REVERT: D 370 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7998 (ttmt) REVERT: C 369 LYS cc_start: 0.7666 (mtpt) cc_final: 0.7193 (mttm) REVERT: E 369 LYS cc_start: 0.7485 (mtpt) cc_final: 0.7118 (mttp) REVERT: F 375 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7817 (tptm) REVERT: G 316 SER cc_start: 0.8248 (p) cc_final: 0.8024 (t) REVERT: G 321 LYS cc_start: 0.7861 (mttt) cc_final: 0.7412 (tttp) REVERT: G 369 LYS cc_start: 0.7387 (mtpt) cc_final: 0.6949 (mttm) REVERT: H 315 LEU cc_start: 0.8111 (mt) cc_final: 0.7721 (mt) REVERT: A 338 GLU cc_start: 0.5519 (mm-30) cc_final: 0.4813 (mm-30) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 1.3504 time to fit residues: 149.3964 Evaluate side-chains 101 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 C residue 375 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 H residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.168974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.145880 restraints weight = 17549.047| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 1.90 r_work: 0.4163 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5686 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= 0.228 Angle : 0.686 6.602 7065 Z= 0.370 Chirality : 0.051 0.137 792 Planarity : 0.006 0.061 900 Dihedral : 6.443 21.481 702 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.20 % Allowed : 18.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 349 TYR 0.013 0.003 TYR A 310 PHE 0.008 0.002 PHE E 378 HIS 0.007 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 5283) covalent geometry : angle 0.68588 ( 7065) hydrogen bonds : bond 0.02821 ( 85) hydrogen bonds : angle 5.15874 ( 255) *********************** 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 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8556 (mt) cc_final: 0.8238 (mm) REVERT: I 349 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6852 (mtp180) REVERT: B 340 LYS cc_start: 0.7935 (tttm) cc_final: 0.7537 (ttmp) REVERT: B 351 GLN cc_start: 0.7935 (tt0) cc_final: 0.7702 (mt0) REVERT: D 321 LYS cc_start: 0.7778 (mttt) cc_final: 0.7505 (ttmm) REVERT: D 370 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8021 (ttmt) REVERT: C 369 LYS cc_start: 0.7685 (mtpt) cc_final: 0.7206 (mttm) REVERT: E 369 LYS cc_start: 0.7519 (mtpt) cc_final: 0.7162 (mttp) REVERT: E 379 ARG cc_start: 0.5340 (mtm180) cc_final: 0.4434 (pmt170) REVERT: F 375 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7822 (tptm) REVERT: G 321 LYS cc_start: 0.7841 (mttt) cc_final: 0.7391 (tttp) REVERT: G 369 LYS cc_start: 0.7390 (mtpt) cc_final: 0.7009 (mttm) REVERT: H 315 LEU cc_start: 0.8124 (mt) cc_final: 0.7722 (mt) REVERT: A 338 GLU cc_start: 0.5493 (mm-30) cc_final: 0.4879 (mm-30) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 1.3972 time to fit residues: 160.5312 Evaluate side-chains 105 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 C residue 375 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 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 Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.166814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.144861 restraints weight = 18462.471| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 1.84 r_work: 0.4138 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5283 Z= 0.274 Angle : 0.731 6.831 7065 Z= 0.393 Chirality : 0.052 0.139 792 Planarity : 0.006 0.062 900 Dihedral : 6.599 22.300 702 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.37 % Allowed : 17.85 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.25), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.19), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 349 TYR 0.015 0.003 TYR A 310 PHE 0.009 0.002 PHE E 378 HIS 0.010 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 5283) covalent geometry : angle 0.73085 ( 7065) hydrogen bonds : bond 0.03202 ( 85) hydrogen bonds : angle 5.31200 ( 255) *********************** 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 110 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8568 (mt) cc_final: 0.8259 (mm) REVERT: I 349 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6947 (mtp180) REVERT: B 340 LYS cc_start: 0.7972 (tttm) cc_final: 0.7578 (ttmp) REVERT: B 349 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6780 (mtp180) REVERT: D 321 LYS cc_start: 0.7819 (mttt) cc_final: 0.7531 (ttmm) REVERT: D 370 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8026 (ttmt) REVERT: C 369 LYS cc_start: 0.7718 (mtpt) cc_final: 0.7250 (mttm) REVERT: E 369 LYS cc_start: 0.7541 (mtpt) cc_final: 0.7197 (mttp) REVERT: E 379 ARG cc_start: 0.5348 (mtm180) cc_final: 0.4523 (pmt170) REVERT: F 311 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8307 (mtmm) REVERT: F 375 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7832 (tptm) REVERT: G 369 LYS cc_start: 0.7492 (mtpt) cc_final: 0.7071 (mttm) REVERT: H 315 LEU cc_start: 0.8155 (mt) cc_final: 0.7753 (mt) REVERT: A 338 GLU cc_start: 0.5564 (mm-30) cc_final: 0.5048 (mm-30) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 1.4064 time to fit residues: 152.4696 Evaluate side-chains 102 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 C residue 375 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 311 LYS 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 A residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.1980 chunk 59 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.173806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.150985 restraints weight = 17234.927| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 1.95 r_work: 0.4231 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4139 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5283 Z= 0.104 Angle : 0.568 7.430 7065 Z= 0.303 Chirality : 0.050 0.133 792 Planarity : 0.005 0.057 900 Dihedral : 5.910 23.390 702 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.68 % Allowed : 19.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (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 ARG 0.010 0.001 ARG E 349 TYR 0.005 0.001 TYR G 310 PHE 0.006 0.001 PHE G 346 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5283) covalent geometry : angle 0.56817 ( 7065) hydrogen bonds : bond 0.01934 ( 85) hydrogen bonds : angle 4.73900 ( 255) *********************** 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: 10 poor density : 101 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8580 (mt) cc_final: 0.8256 (mm) REVERT: I 349 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6850 (mtp180) REVERT: I 369 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7916 (mtmm) REVERT: D 321 LYS cc_start: 0.7722 (mttt) cc_final: 0.7455 (ttmm) REVERT: D 331 LYS cc_start: 0.8234 (mttp) cc_final: 0.8014 (mtpt) REVERT: C 369 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7190 (mttm) REVERT: C 375 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7326 (ttpt) REVERT: E 369 LYS cc_start: 0.7414 (mtpt) cc_final: 0.7048 (mttp) REVERT: E 379 ARG cc_start: 0.5208 (mtm180) cc_final: 0.4438 (pmt170) REVERT: F 375 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7765 (tptm) REVERT: G 369 LYS cc_start: 0.7323 (mtpt) cc_final: 0.6882 (mttm) REVERT: H 315 LEU cc_start: 0.8128 (mt) cc_final: 0.7697 (mt) outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 1.4695 time to fit residues: 164.0378 Evaluate side-chains 99 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER 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 C residue 375 LYS Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 9.9990 chunk 4 optimal weight: 0.0670 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- 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 = 0.4527 r_free = 0.4527 target = 0.172918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.150376 restraints weight = 17140.461| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 1.85 r_work: 0.4217 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.6090 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= 0.128 Angle : 0.581 7.519 7065 Z= 0.310 Chirality : 0.050 0.130 792 Planarity : 0.005 0.060 900 Dihedral : 5.785 22.118 702 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.68 % Allowed : 20.37 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (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 ARG 0.010 0.001 ARG E 349 TYR 0.009 0.002 TYR G 310 PHE 0.011 0.001 PHE A 346 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5283) covalent geometry : angle 0.58078 ( 7065) hydrogen bonds : bond 0.02032 ( 85) hydrogen bonds : angle 4.68949 ( 255) *********************** 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: 10 poor density : 99 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8580 (mt) cc_final: 0.8263 (mm) REVERT: I 349 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6868 (mtp180) REVERT: I 369 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7927 (mtmm) REVERT: B 340 LYS cc_start: 0.7861 (tttm) cc_final: 0.7643 (ttmm) REVERT: D 321 LYS cc_start: 0.7749 (mttt) cc_final: 0.7522 (ttmm) REVERT: D 331 LYS cc_start: 0.8209 (mttp) cc_final: 0.7984 (mtpt) REVERT: C 369 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7197 (mttm) REVERT: E 369 LYS cc_start: 0.7459 (mtpt) cc_final: 0.7107 (mttp) REVERT: E 379 ARG cc_start: 0.5260 (mtm180) cc_final: 0.4470 (pmt170) REVERT: F 375 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7788 (tptm) REVERT: G 369 LYS cc_start: 0.7364 (mtpt) cc_final: 0.6958 (mttm) REVERT: A 349 ARG cc_start: 0.4603 (mmp-170) cc_final: 0.3405 (mtp85) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 1.4474 time to fit residues: 161.3444 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 : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER 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 320 SER Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.172990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.150315 restraints weight = 17215.763| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 1.88 r_work: 0.4223 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6112 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= 0.128 Angle : 0.590 7.915 7065 Z= 0.313 Chirality : 0.050 0.129 792 Planarity : 0.006 0.063 900 Dihedral : 5.776 21.730 702 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.18 % Allowed : 21.72 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (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 ARG 0.012 0.001 ARG E 349 TYR 0.009 0.002 TYR G 310 PHE 0.005 0.001 PHE D 378 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5283) covalent geometry : angle 0.59039 ( 7065) hydrogen bonds : bond 0.02007 ( 85) hydrogen bonds : angle 4.68719 ( 255) ********************** 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 104 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 308 ILE cc_start: 0.8576 (mt) cc_final: 0.8260 (mm) REVERT: I 349 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6886 (mtp180) REVERT: I 369 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7926 (mtmm) REVERT: B 340 LYS cc_start: 0.7882 (tttm) cc_final: 0.7659 (ttmm) REVERT: D 321 LYS cc_start: 0.7746 (mttt) cc_final: 0.7536 (ttmm) REVERT: D 331 LYS cc_start: 0.8225 (mttp) cc_final: 0.8003 (mtpt) REVERT: C 369 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7188 (mttm) REVERT: E 369 LYS cc_start: 0.7468 (mtpt) cc_final: 0.7116 (mttp) REVERT: E 379 ARG cc_start: 0.5252 (mtm180) cc_final: 0.4486 (pmt170) REVERT: F 375 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7808 (tptm) REVERT: G 369 LYS cc_start: 0.7362 (mtpt) cc_final: 0.6948 (mttm) outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 1.4367 time to fit residues: 151.4556 Evaluate side-chains 102 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 320 SER 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 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 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- 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 = 0.4535 r_free = 0.4535 target = 0.173945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.151338 restraints weight = 17284.154| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 1.88 r_work: 0.4237 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6198 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= 0.119 Angle : 0.573 7.900 7065 Z= 0.302 Chirality : 0.050 0.128 792 Planarity : 0.005 0.060 900 Dihedral : 5.611 22.015 702 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.35 % Allowed : 21.21 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.26), residues: 666 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.20), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 349 TYR 0.007 0.001 TYR G 310 PHE 0.014 0.001 PHE A 346 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5283) covalent geometry : angle 0.57336 ( 7065) hydrogen bonds : bond 0.01909 ( 85) hydrogen bonds : angle 4.63363 ( 255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4825.33 seconds wall clock time: 82 minutes 30.36 seconds (4950.36 seconds total)