Starting phenix.real_space_refine on Mon Mar 11 00:35:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql0_14059/03_2024/7ql0_14059.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql0_14059/03_2024/7ql0_14059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql0_14059/03_2024/7ql0_14059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql0_14059/03_2024/7ql0_14059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql0_14059/03_2024/7ql0_14059.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql0_14059/03_2024/7ql0_14059.pdb" } resolution = 3.13 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 6 5.16 5 C 1956 2.51 5 N 576 2.21 5 O 594 1.98 5 H 3258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 338": "OE1" <-> "OE2" Residue "c PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6390 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "c" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "A" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "D" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "E" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Time building chain proxies: 3.14, per 1000 atoms: 0.49 Number of scatterers: 6390 At special positions: 0 Unit cell: (93.936, 127.72, 34.608, 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 6 16.00 O 594 8.00 N 576 7.00 C 1956 6.00 H 3258 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 - 3.50 Amino acid : False - 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: 4.40 Conformation dependent library (CDL) restraints added in 602.1 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'c' and resid 313 through 314 removed outlier: 6.878A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 317 through 318 removed outlier: 6.340A pdb=" N LYS B 317 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 325 through 330 removed outlier: 6.273A pdb=" N GLY B 326 " --> pdb=" O ASN c 327 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N HIS c 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 328 " --> pdb=" O HIS c 329 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY A 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 337 through 342 removed outlier: 6.649A pdb=" N VAL B 337 " --> pdb=" O GLU c 338 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LYS c 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 339 " --> pdb=" O LYS c 340 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU c 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER B 341 " --> pdb=" O GLU c 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 345 through 346 removed outlier: 6.465A pdb=" N ASP B 345 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 350 through 357 removed outlier: 6.243A pdb=" N VAL B 350 " --> pdb=" O GLN c 351 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LYS c 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B 352 " --> pdb=" O LYS c 353 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY c 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 354 " --> pdb=" O GLY c 355 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU c 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER B 356 " --> pdb=" O LEU c 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 360 through 362 removed outlier: 6.432A pdb=" N THR B 361 " --> pdb=" O HIS c 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 369 through 375 removed outlier: 6.544A pdb=" N LYS B 369 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU A 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B 371 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N HIS A 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR B 373 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.794A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 318 removed outlier: 6.522A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 324 through 330 removed outlier: 9.443A pdb=" N SER C 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N ASN D 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY E 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 342 Processing sheet with id=AB4, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.495A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.215A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS D 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER C 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLY D 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER C 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.539A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 371 removed outlier: 6.388A pdb=" N LYS C 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3252 1.11 - 1.29: 528 1.29 - 1.46: 885 1.46 - 1.64: 1767 1.64 - 1.82: 6 Bond restraints: 6438 Sorted by residual: bond pdb=" CE1 HIS B 330 " pdb=" HE1 HIS B 330 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LYS c 311 " pdb=" H LYS c 311 " 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 E 326 " pdb=" H GLY E 326 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE E 328 " pdb=" H ILE E 328 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER A 356 " pdb=" H SER A 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6433 not shown) Histogram of bond angle deviations from ideal: 96.88 - 103.34: 36 103.34 - 109.80: 5508 109.80 - 116.26: 2993 116.26 - 122.72: 2611 122.72 - 129.18: 606 Bond angle restraints: 11754 Sorted by residual: angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.69 118.23 -7.54 1.33e+00 5.65e-01 3.21e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.74 117.48 -6.74 1.37e+00 5.33e-01 2.42e+01 angle pdb=" C ASP c 348 " pdb=" N ARG c 349 " pdb=" CA ARG c 349 " ideal model delta sigma weight residual 121.56 129.18 -7.62 1.56e+00 4.11e-01 2.39e+01 angle pdb=" C ASP D 348 " pdb=" N ARG D 349 " pdb=" CA ARG D 349 " ideal model delta sigma weight residual 121.31 128.35 -7.04 1.49e+00 4.50e-01 2.23e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 125.41 5.79 1.30e+00 5.92e-01 1.98e+01 ... (remaining 11749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 2623 16.08 - 32.16: 148 32.16 - 48.25: 69 48.25 - 64.33: 118 64.33 - 80.41: 6 Dihedral angle restraints: 2964 sinusoidal: 1704 harmonic: 1260 Sorted by residual: dihedral pdb=" CA GLN A 336 " pdb=" C GLN A 336 " pdb=" N VAL A 337 " pdb=" CA VAL A 337 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA LYS E 375 " pdb=" C LYS E 375 " pdb=" N LEU E 376 " pdb=" CA LEU E 376 " ideal model delta harmonic sigma weight residual 180.00 153.45 26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N THR C 319 " pdb=" CA THR C 319 " ideal model delta harmonic sigma weight residual 180.00 -154.58 -25.42 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 2961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 282 0.070 - 0.139: 147 0.139 - 0.208: 36 0.208 - 0.278: 10 0.278 - 0.347: 5 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA ASN D 327 " pdb=" N ASN D 327 " pdb=" C ASN D 327 " pdb=" CB ASN D 327 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA LYS D 321 " pdb=" N LYS D 321 " pdb=" C LYS D 321 " pdb=" CB LYS D 321 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ASN C 327 " pdb=" N ASN C 327 " pdb=" C ASN C 327 " pdb=" CB ASN C 327 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 477 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR c 310 " -0.149 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" CG TYR c 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR c 310 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR c 310 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR c 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR c 310 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR c 310 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR c 310 " -0.099 2.00e-02 2.50e+03 pdb=" HD1 TYR c 310 " 0.059 2.00e-02 2.50e+03 pdb=" HD2 TYR c 310 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 TYR c 310 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR c 310 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.149 2.00e-02 2.50e+03 5.96e-02 1.07e+02 pdb=" CG TYR E 310 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.095 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " -0.064 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.139 2.00e-02 2.50e+03 5.47e-02 8.98e+01 pdb=" CG TYR C 310 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.067 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.018 2.00e-02 2.50e+03 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 424 2.17 - 2.77: 11012 2.77 - 3.38: 16927 3.38 - 3.99: 22645 3.99 - 4.60: 31452 Nonbonded interactions: 82460 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.557 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.558 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.558 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.596 1.850 ... (remaining 82455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.090 Extract box with map and model: 10.890 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.790 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 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 0.035 3180 Z= 0.747 Angle : 1.875 7.621 4254 Z= 1.238 Chirality : 0.093 0.347 480 Planarity : 0.011 0.068 540 Dihedral : 12.058 80.411 1224 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.005 HIS D 362 PHE 0.046 0.015 PHE A 346 TYR 0.128 0.046 TYR c 310 ARG 0.006 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7708 (mtmt) cc_final: 0.7232 (mttm) REVERT: B 345 ASP cc_start: 0.7855 (m-30) cc_final: 0.7438 (t0) REVERT: B 347 LYS cc_start: 0.8736 (mttt) cc_final: 0.8320 (mtpt) REVERT: c 311 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7363 (mmtt) REVERT: A 310 TYR cc_start: 0.6480 (t80) cc_final: 0.6174 (t80) REVERT: A 311 LYS cc_start: 0.7317 (mtmt) cc_final: 0.7076 (mttp) REVERT: A 345 ASP cc_start: 0.8253 (m-30) cc_final: 0.8015 (t0) REVERT: A 347 LYS cc_start: 0.8685 (mttt) cc_final: 0.8282 (mtpt) REVERT: A 348 ASP cc_start: 0.8307 (t70) cc_final: 0.7492 (p0) REVERT: A 349 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7304 (pmt-80) REVERT: A 375 LYS cc_start: 0.7516 (tttt) cc_final: 0.7044 (tttm) REVERT: D 311 LYS cc_start: 0.6375 (mtmt) cc_final: 0.5530 (mmtm) REVERT: D 349 ARG cc_start: 0.6886 (mtm180) cc_final: 0.6646 (mmp-170) REVERT: E 317 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7387 (mttm) REVERT: E 343 LYS cc_start: 0.8872 (mttt) cc_final: 0.8639 (mttp) REVERT: E 349 ARG cc_start: 0.7244 (mtm180) cc_final: 0.6352 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.4687 time to fit residues: 51.2604 Evaluate side-chains 55 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS c 362 HIS A 362 HIS C 362 HIS D 362 HIS E 351 GLN E 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3180 Z= 0.173 Angle : 0.652 6.177 4254 Z= 0.336 Chirality : 0.051 0.132 480 Planarity : 0.002 0.015 540 Dihedral : 7.430 20.573 420 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 0.56 % Allowed : 8.89 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.006 0.001 PHE B 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7216 (mttm) REVERT: B 345 ASP cc_start: 0.7871 (m-30) cc_final: 0.7451 (t0) REVERT: B 347 LYS cc_start: 0.8856 (mttt) cc_final: 0.8471 (mtpt) REVERT: c 311 LYS cc_start: 0.7861 (mtmt) cc_final: 0.7461 (mmtt) REVERT: A 310 TYR cc_start: 0.6655 (t80) cc_final: 0.6285 (t80) REVERT: A 311 LYS cc_start: 0.7351 (mtmt) cc_final: 0.7114 (mttp) REVERT: A 321 LYS cc_start: 0.8146 (mttt) cc_final: 0.7389 (tmtt) REVERT: A 347 LYS cc_start: 0.8784 (mttt) cc_final: 0.8467 (mtpt) REVERT: A 348 ASP cc_start: 0.8316 (t70) cc_final: 0.7195 (p0) REVERT: A 349 ARG cc_start: 0.7486 (mtm180) cc_final: 0.7066 (pmt-80) REVERT: A 372 GLU cc_start: 0.7563 (tt0) cc_final: 0.6993 (mt-10) REVERT: C 349 ARG cc_start: 0.7374 (mtp180) cc_final: 0.7133 (mtm-85) REVERT: D 349 ARG cc_start: 0.7022 (mtm180) cc_final: 0.6634 (mmp-170) REVERT: E 316 SER cc_start: 0.7746 (OUTLIER) cc_final: 0.7532 (p) REVERT: E 343 LYS cc_start: 0.8985 (mttt) cc_final: 0.8740 (mttp) REVERT: E 349 ARG cc_start: 0.7519 (mtm180) cc_final: 0.6320 (pmt-80) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.5293 time to fit residues: 40.0069 Evaluate side-chains 53 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 315 LEU Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 359 ASN D 359 ASN E 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3180 Z= 0.131 Angle : 0.533 5.897 4254 Z= 0.274 Chirality : 0.050 0.149 480 Planarity : 0.002 0.011 540 Dihedral : 5.863 16.251 420 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.11 % Allowed : 10.00 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.006 0.001 PHE A 346 TYR 0.014 0.002 TYR E 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7624 (mtmt) cc_final: 0.7247 (mttm) REVERT: B 321 LYS cc_start: 0.7902 (mttt) cc_final: 0.7160 (tttm) REVERT: B 345 ASP cc_start: 0.7652 (m-30) cc_final: 0.7361 (t0) REVERT: B 347 LYS cc_start: 0.8752 (mttt) cc_final: 0.8379 (mtpt) REVERT: B 372 GLU cc_start: 0.6845 (tt0) cc_final: 0.6208 (mt-10) REVERT: B 375 LYS cc_start: 0.6447 (tttt) cc_final: 0.6112 (tttm) REVERT: c 311 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7497 (mmtt) REVERT: A 310 TYR cc_start: 0.6789 (t80) cc_final: 0.6286 (t80) REVERT: A 311 LYS cc_start: 0.7325 (mtmt) cc_final: 0.7071 (mttp) REVERT: A 321 LYS cc_start: 0.8150 (mttt) cc_final: 0.7402 (tttm) REVERT: A 347 LYS cc_start: 0.8690 (mttt) cc_final: 0.8329 (mtpt) REVERT: A 348 ASP cc_start: 0.8464 (t70) cc_final: 0.7568 (p0) REVERT: A 349 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7062 (pmt-80) REVERT: A 372 GLU cc_start: 0.7885 (tt0) cc_final: 0.7338 (mt-10) REVERT: C 349 ARG cc_start: 0.7411 (mtp180) cc_final: 0.7199 (mtm110) REVERT: D 349 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6808 (mmp-170) REVERT: E 343 LYS cc_start: 0.9037 (mttt) cc_final: 0.8791 (mttp) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.5415 time to fit residues: 37.2684 Evaluate side-chains 56 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3180 Z= 0.225 Angle : 0.535 5.616 4254 Z= 0.278 Chirality : 0.050 0.134 480 Planarity : 0.002 0.013 540 Dihedral : 5.735 16.052 420 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 1.11 % Allowed : 10.83 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 374 PHE 0.005 0.001 PHE A 346 TYR 0.017 0.003 TYR C 310 ARG 0.002 0.001 ARG c 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7283 (mttm) REVERT: B 321 LYS cc_start: 0.7989 (mttt) cc_final: 0.7297 (tttm) REVERT: B 345 ASP cc_start: 0.7766 (m-30) cc_final: 0.7380 (t0) REVERT: B 347 LYS cc_start: 0.8818 (mttt) cc_final: 0.8433 (mtpt) REVERT: B 372 GLU cc_start: 0.6833 (tt0) cc_final: 0.6508 (mt-10) REVERT: B 375 LYS cc_start: 0.6576 (tttt) cc_final: 0.6260 (tttm) REVERT: c 311 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7473 (mmtt) REVERT: c 347 LYS cc_start: 0.8942 (mttt) cc_final: 0.8491 (mtpt) REVERT: A 311 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6979 (mttp) REVERT: A 321 LYS cc_start: 0.8237 (mttt) cc_final: 0.7453 (tttm) REVERT: A 347 LYS cc_start: 0.8746 (mttt) cc_final: 0.8383 (mtpt) REVERT: A 348 ASP cc_start: 0.8557 (t70) cc_final: 0.7617 (p0) REVERT: A 349 ARG cc_start: 0.7683 (mtm180) cc_final: 0.7226 (pmt-80) REVERT: C 349 ARG cc_start: 0.7385 (mtp180) cc_final: 0.7026 (mtm110) REVERT: D 349 ARG cc_start: 0.7297 (mtm180) cc_final: 0.6907 (mmp-170) REVERT: E 343 LYS cc_start: 0.9043 (mttt) cc_final: 0.8798 (mttp) REVERT: E 349 ARG cc_start: 0.7584 (mtm180) cc_final: 0.6405 (pmt-80) outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.5286 time to fit residues: 35.9001 Evaluate side-chains 57 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.0770 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3180 Z= 0.209 Angle : 0.523 5.948 4254 Z= 0.271 Chirality : 0.049 0.133 480 Planarity : 0.002 0.012 540 Dihedral : 5.455 15.892 420 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.67 % Allowed : 10.56 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 374 PHE 0.004 0.001 PHE B 346 TYR 0.020 0.003 TYR D 310 ARG 0.002 0.001 ARG c 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7249 (mttm) REVERT: B 321 LYS cc_start: 0.8063 (mttt) cc_final: 0.7351 (tttm) REVERT: B 345 ASP cc_start: 0.7735 (m-30) cc_final: 0.7470 (t0) REVERT: B 347 LYS cc_start: 0.8849 (mttt) cc_final: 0.8407 (mtpt) REVERT: B 372 GLU cc_start: 0.6969 (tt0) cc_final: 0.6617 (mt-10) REVERT: B 375 LYS cc_start: 0.6648 (tttt) cc_final: 0.6253 (tttm) REVERT: c 311 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7455 (mmtt) REVERT: c 347 LYS cc_start: 0.8965 (mttt) cc_final: 0.8485 (mtpt) REVERT: A 311 LYS cc_start: 0.7309 (mtmt) cc_final: 0.6992 (mttp) REVERT: A 321 LYS cc_start: 0.8327 (mttt) cc_final: 0.7508 (tttm) REVERT: A 347 LYS cc_start: 0.8756 (mttt) cc_final: 0.8375 (mtpt) REVERT: A 348 ASP cc_start: 0.8618 (t70) cc_final: 0.7636 (p0) REVERT: A 349 ARG cc_start: 0.7709 (mtm180) cc_final: 0.7200 (pmt-80) REVERT: C 349 ARG cc_start: 0.7418 (mtp180) cc_final: 0.7048 (mtm110) REVERT: D 349 ARG cc_start: 0.7332 (mtm180) cc_final: 0.6909 (mmp-170) REVERT: E 343 LYS cc_start: 0.9019 (mttt) cc_final: 0.8627 (mttp) REVERT: E 349 ARG cc_start: 0.7577 (mtm180) cc_final: 0.6417 (pmt-80) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.5497 time to fit residues: 36.5856 Evaluate side-chains 58 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3180 Z= 0.225 Angle : 0.519 5.299 4254 Z= 0.268 Chirality : 0.049 0.136 480 Planarity : 0.002 0.012 540 Dihedral : 5.362 15.663 420 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.67 % Allowed : 10.56 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.004 0.001 PHE B 346 TYR 0.017 0.003 TYR C 310 ARG 0.002 0.001 ARG c 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7646 (mtmt) cc_final: 0.7219 (mttp) REVERT: B 321 LYS cc_start: 0.8151 (mttt) cc_final: 0.7439 (tttm) REVERT: B 345 ASP cc_start: 0.7764 (m-30) cc_final: 0.7519 (t0) REVERT: B 347 LYS cc_start: 0.8809 (mttt) cc_final: 0.8356 (mtpt) REVERT: B 375 LYS cc_start: 0.6721 (tttt) cc_final: 0.6340 (tttm) REVERT: c 311 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7477 (mmtm) REVERT: c 347 LYS cc_start: 0.8955 (mttt) cc_final: 0.8469 (mtpt) REVERT: c 377 THR cc_start: 0.5394 (OUTLIER) cc_final: 0.5137 (p) REVERT: A 311 LYS cc_start: 0.7373 (mtmt) cc_final: 0.7061 (mttp) REVERT: A 321 LYS cc_start: 0.8385 (mttt) cc_final: 0.7551 (tttm) REVERT: A 347 LYS cc_start: 0.8798 (mttt) cc_final: 0.8398 (mtpt) REVERT: A 348 ASP cc_start: 0.8629 (t70) cc_final: 0.7632 (p0) REVERT: A 349 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7244 (pmt-80) REVERT: C 349 ARG cc_start: 0.7432 (mtp180) cc_final: 0.7040 (mtm110) REVERT: D 349 ARG cc_start: 0.7347 (mtm180) cc_final: 0.6963 (mmp-170) REVERT: E 343 LYS cc_start: 0.8993 (mttt) cc_final: 0.8607 (mttp) REVERT: E 349 ARG cc_start: 0.7580 (mtm180) cc_final: 0.6426 (pmt-80) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.5399 time to fit residues: 34.9200 Evaluate side-chains 56 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3180 Z= 0.186 Angle : 0.500 5.236 4254 Z= 0.257 Chirality : 0.049 0.133 480 Planarity : 0.002 0.011 540 Dihedral : 5.155 15.809 420 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.67 % Allowed : 11.39 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.003 0.001 PHE B 346 TYR 0.014 0.002 TYR C 310 ARG 0.002 0.000 ARG c 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7230 (mttp) REVERT: B 321 LYS cc_start: 0.8135 (mttt) cc_final: 0.7453 (tttm) REVERT: B 345 ASP cc_start: 0.7756 (m-30) cc_final: 0.7514 (t0) REVERT: B 347 LYS cc_start: 0.8798 (mttt) cc_final: 0.8348 (mtpt) REVERT: B 375 LYS cc_start: 0.6843 (tttt) cc_final: 0.6458 (tttm) REVERT: c 311 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7487 (mmtm) REVERT: c 347 LYS cc_start: 0.8948 (mttt) cc_final: 0.8461 (mtpt) REVERT: c 377 THR cc_start: 0.5446 (OUTLIER) cc_final: 0.5167 (p) REVERT: A 311 LYS cc_start: 0.7396 (mtmt) cc_final: 0.7079 (mttp) REVERT: A 321 LYS cc_start: 0.8389 (mttt) cc_final: 0.7551 (tttm) REVERT: A 347 LYS cc_start: 0.8782 (mttt) cc_final: 0.8393 (mtpt) REVERT: A 348 ASP cc_start: 0.8633 (t70) cc_final: 0.7670 (p0) REVERT: A 349 ARG cc_start: 0.7780 (mtm180) cc_final: 0.7259 (pmt-80) REVERT: C 349 ARG cc_start: 0.7456 (mtp180) cc_final: 0.7064 (mtm110) REVERT: D 349 ARG cc_start: 0.7364 (mtm180) cc_final: 0.6992 (mmp-170) REVERT: E 343 LYS cc_start: 0.8989 (mttt) cc_final: 0.8617 (mttp) REVERT: E 349 ARG cc_start: 0.7580 (mtm180) cc_final: 0.6427 (pmt-80) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.5378 time to fit residues: 32.5881 Evaluate side-chains 54 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3180 Z= 0.161 Angle : 0.487 5.199 4254 Z= 0.250 Chirality : 0.049 0.132 480 Planarity : 0.002 0.010 540 Dihedral : 5.007 15.587 420 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.67 % Allowed : 11.67 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.003 0.001 PHE B 346 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG c 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7628 (mtmt) cc_final: 0.7212 (mttp) REVERT: B 321 LYS cc_start: 0.8143 (mttt) cc_final: 0.7461 (tttm) REVERT: B 345 ASP cc_start: 0.7787 (m-30) cc_final: 0.7524 (t0) REVERT: B 347 LYS cc_start: 0.8785 (mttt) cc_final: 0.8332 (mtpt) REVERT: B 375 LYS cc_start: 0.6852 (tttt) cc_final: 0.6488 (tttm) REVERT: c 311 LYS cc_start: 0.7886 (mtmt) cc_final: 0.7515 (mmtm) REVERT: c 347 LYS cc_start: 0.8938 (mttt) cc_final: 0.8445 (mtpt) REVERT: c 377 THR cc_start: 0.5437 (OUTLIER) cc_final: 0.5158 (p) REVERT: A 311 LYS cc_start: 0.7385 (mtmt) cc_final: 0.7064 (mttp) REVERT: A 321 LYS cc_start: 0.8395 (mttt) cc_final: 0.7578 (tttm) REVERT: A 347 LYS cc_start: 0.8780 (mttt) cc_final: 0.8388 (mtpt) REVERT: A 348 ASP cc_start: 0.8567 (t70) cc_final: 0.7627 (p0) REVERT: A 349 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7256 (pmt-80) REVERT: C 349 ARG cc_start: 0.7463 (mtp180) cc_final: 0.7070 (mtm110) REVERT: D 349 ARG cc_start: 0.7374 (mtm180) cc_final: 0.6954 (mmp-170) REVERT: E 343 LYS cc_start: 0.8994 (mttt) cc_final: 0.8622 (mttp) REVERT: E 349 ARG cc_start: 0.7559 (mtm180) cc_final: 0.6425 (pmt-80) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.5704 time to fit residues: 34.2353 Evaluate side-chains 52 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.0030 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3180 Z= 0.127 Angle : 0.466 5.200 4254 Z= 0.238 Chirality : 0.049 0.129 480 Planarity : 0.002 0.012 540 Dihedral : 4.766 15.155 420 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.39 % Allowed : 12.50 % Favored : 86.11 % 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: -1.73 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.002 0.001 PHE E 346 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG c 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7174 (mttp) REVERT: B 321 LYS cc_start: 0.8121 (mttt) cc_final: 0.7432 (tttm) REVERT: B 345 ASP cc_start: 0.7778 (m-30) cc_final: 0.7505 (t0) REVERT: B 347 LYS cc_start: 0.8743 (mttt) cc_final: 0.8289 (mtpt) REVERT: B 375 LYS cc_start: 0.6811 (tttt) cc_final: 0.6428 (tttm) REVERT: c 311 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7545 (mmtm) REVERT: c 347 LYS cc_start: 0.8914 (mttt) cc_final: 0.8410 (mtpt) REVERT: c 377 THR cc_start: 0.5306 (OUTLIER) cc_final: 0.5043 (p) REVERT: A 311 LYS cc_start: 0.7392 (mtmt) cc_final: 0.7109 (mttp) REVERT: A 321 LYS cc_start: 0.8370 (mttt) cc_final: 0.7552 (tttm) REVERT: A 347 LYS cc_start: 0.8773 (mttt) cc_final: 0.8387 (mtpt) REVERT: A 348 ASP cc_start: 0.8559 (t70) cc_final: 0.7591 (p0) REVERT: A 349 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7265 (pmt-80) REVERT: C 349 ARG cc_start: 0.7473 (mtp180) cc_final: 0.7094 (mtm110) REVERT: D 349 ARG cc_start: 0.7400 (mtm180) cc_final: 0.6984 (mmp-170) REVERT: E 343 LYS cc_start: 0.9002 (mttt) cc_final: 0.8633 (mttp) REVERT: E 349 ARG cc_start: 0.7575 (mtm180) cc_final: 0.6422 (pmt-80) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.5919 time to fit residues: 37.5743 Evaluate side-chains 52 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain D residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.0040 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 3180 Z= 0.093 Angle : 0.446 5.219 4254 Z= 0.227 Chirality : 0.049 0.125 480 Planarity : 0.002 0.017 540 Dihedral : 4.449 14.489 420 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.39 % Allowed : 12.78 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.002 0.001 PHE E 346 TYR 0.007 0.001 TYR c 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: B 311 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7144 (mttp) REVERT: B 321 LYS cc_start: 0.8171 (mttt) cc_final: 0.7495 (tttm) REVERT: B 345 ASP cc_start: 0.7827 (m-30) cc_final: 0.7558 (t0) REVERT: B 347 LYS cc_start: 0.8701 (mttt) cc_final: 0.8249 (mtpt) REVERT: B 375 LYS cc_start: 0.6812 (tttt) cc_final: 0.6428 (tttm) REVERT: c 311 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7598 (mmtt) REVERT: c 347 LYS cc_start: 0.8888 (mttt) cc_final: 0.8383 (mtpt) REVERT: c 377 THR cc_start: 0.5438 (OUTLIER) cc_final: 0.5157 (p) REVERT: A 311 LYS cc_start: 0.7410 (mtmt) cc_final: 0.7130 (mttp) REVERT: A 321 LYS cc_start: 0.8352 (mttt) cc_final: 0.7544 (tttm) REVERT: A 347 LYS cc_start: 0.8773 (mttt) cc_final: 0.8363 (mtpt) REVERT: A 348 ASP cc_start: 0.8515 (t70) cc_final: 0.7526 (p0) REVERT: A 349 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7268 (pmt-80) REVERT: C 349 ARG cc_start: 0.7441 (mtp180) cc_final: 0.7185 (mtm110) REVERT: D 349 ARG cc_start: 0.7414 (mtm180) cc_final: 0.6929 (mmp-170) REVERT: E 343 LYS cc_start: 0.8984 (mttt) cc_final: 0.8701 (mttp) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 0.4910 time to fit residues: 33.1600 Evaluate side-chains 54 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 THR Chi-restraints excluded: chain D residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.145142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.117670 restraints weight = 11858.463| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.17 r_work: 0.4097 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4016 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 3180 Z= 0.094 Angle : 0.447 5.105 4254 Z= 0.226 Chirality : 0.049 0.127 480 Planarity : 0.002 0.015 540 Dihedral : 4.351 14.167 420 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.39 % Allowed : 13.89 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.002 0.001 PHE E 346 TYR 0.007 0.001 TYR D 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2830.36 seconds wall clock time: 51 minutes 10.94 seconds (3070.94 seconds total)