Starting phenix.real_space_refine on Mon Mar 11 04:45:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/03_2024/8q2k_18111.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/03_2024/8q2k_18111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/03_2024/8q2k_18111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/03_2024/8q2k_18111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/03_2024/8q2k_18111.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/03_2024/8q2k_18111.pdb" } resolution = 2.88 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= 0.004 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 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 358": "OD1" <-> "OD2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 358": "OD1" <-> "OD2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 358": "OD1" <-> "OD2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.86, per 1000 atoms: 0.55 Number of scatterers: 7032 At special positions: 0 Unit cell: (132.314, 111.958, 41.439, 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 642 8.00 N 636 7.00 C 2160 6.00 H 3588 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: 4.93 Conformation dependent library (CDL) restraints added in 720.5 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 48.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.525A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.849A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.474A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.690A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.529A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER C 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS A 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.504A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.382A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.399A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.427A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 376 through 378 removed outlier: 6.654A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.561A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.884A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.512A pdb=" N HIS B 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 342 Processing sheet with id=AB7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.664A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.404A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.606A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.477A pdb=" N ASN B 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE F 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 376 through 378 removed outlier: 6.756A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 258 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: 2.17 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3582 1.12 - 1.29: 570 1.29 - 1.46: 1059 1.46 - 1.64: 1869 1.64 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" N ARG D 349 " pdb=" H ARG D 349 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CE1 HIS F 374 " pdb=" HE1 HIS F 374 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N GLU B 372 " pdb=" H GLU B 372 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CD2 HIS F 362 " pdb=" HD2 HIS F 362 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" ND1 HIS C 362 " pdb=" HD1 HIS C 362 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 95.83 - 102.58: 18 102.58 - 109.34: 4843 109.34 - 116.10: 4398 116.10 - 122.85: 3002 122.85 - 129.61: 651 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " pdb=" CD2 HIS D 374 " ideal model delta sigma weight residual 131.20 124.51 6.69 1.30e+00 5.92e-01 2.65e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 124.61 6.59 1.30e+00 5.92e-01 2.57e+01 angle pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " pdb=" CD2 HIS C 374 " ideal model delta sigma weight residual 131.20 124.64 6.56 1.30e+00 5.92e-01 2.55e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 124.76 6.44 1.30e+00 5.92e-01 2.45e+01 angle pdb=" C ASP E 314 " pdb=" N LEU E 315 " pdb=" CA LEU E 315 " ideal model delta sigma weight residual 122.37 129.17 -6.80 1.54e+00 4.22e-01 1.95e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 2914 15.15 - 30.31: 169 30.31 - 45.46: 69 45.46 - 60.61: 66 60.61 - 75.76: 46 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA GLN A 307 " pdb=" C GLN A 307 " pdb=" N ILE A 308 " pdb=" CA ILE A 308 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" C LYS F 343 " pdb=" N LYS F 343 " pdb=" CA LYS F 343 " pdb=" CB LYS F 343 " ideal model delta harmonic sigma weight residual -122.60 -130.95 8.35 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" CA THR F 319 " pdb=" C THR F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.050: 242 0.050 - 0.099: 214 0.099 - 0.148: 57 0.148 - 0.197: 12 0.197 - 0.246: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 343 " pdb=" N LYS F 343 " pdb=" C LYS F 343 " pdb=" CB LYS F 343 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA LYS E 331 " pdb=" N LYS E 331 " pdb=" C LYS E 331 " pdb=" CB LYS E 331 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LYS E 343 " pdb=" N LYS E 343 " pdb=" C LYS E 343 " pdb=" CB LYS E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 374 " -0.095 2.00e-02 2.50e+03 5.49e-02 6.77e+01 pdb=" CG HIS D 374 " 0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS D 374 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS D 374 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS D 374 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS D 374 " 0.030 2.00e-02 2.50e+03 pdb=" HD2 HIS D 374 " 0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS D 374 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 HIS D 374 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " 0.086 2.00e-02 2.50e+03 5.13e-02 5.92e+01 pdb=" CG HIS A 374 " -0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 374 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 HIS A 374 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 HIS A 374 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " 0.089 2.00e-02 2.50e+03 5.13e-02 5.92e+01 pdb=" CG HIS C 374 " -0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " 0.027 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " 0.085 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 603 2.18 - 2.79: 12295 2.79 - 3.39: 18077 3.39 - 4.00: 25062 4.00 - 4.60: 34061 Nonbonded interactions: 90098 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.579 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.582 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.588 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.591 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.627 1.850 ... (remaining 90093 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 'F' } 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: 3.360 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: 0.110 Extract box with map and model: 11.770 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.400 Find NCS groups from input model: 0.330 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.034 3498 Z= 0.750 Angle : 1.799 6.798 4680 Z= 1.181 Chirality : 0.070 0.246 528 Planarity : 0.009 0.040 594 Dihedral : 10.493 67.213 1344 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.81 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.004 HIS B 362 PHE 0.057 0.020 PHE C 346 TYR 0.046 0.009 TYR E 310 ARG 0.005 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.585 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: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.6833 (tt0) cc_final: 0.6071 (tp30) REVERT: A 345 ASP cc_start: 0.7509 (t0) cc_final: 0.7099 (m-30) REVERT: A 353 LYS cc_start: 0.6953 (mttt) cc_final: 0.6643 (tmtp) REVERT: A 369 LYS cc_start: 0.6927 (tttt) cc_final: 0.6665 (ttpt) REVERT: B 336 GLN cc_start: 0.8112 (tt0) cc_final: 0.7902 (tt0) REVERT: B 338 GLU cc_start: 0.7620 (tt0) cc_final: 0.7357 (tt0) REVERT: B 340 LYS cc_start: 0.7237 (tttt) cc_final: 0.6328 (tmtm) REVERT: B 342 GLU cc_start: 0.7244 (tt0) cc_final: 0.6922 (tt0) REVERT: B 353 LYS cc_start: 0.6929 (mttt) cc_final: 0.6693 (tttm) REVERT: C 317 LYS cc_start: 0.7883 (mttt) cc_final: 0.7527 (mtpt) REVERT: C 338 GLU cc_start: 0.7478 (tt0) cc_final: 0.6733 (tp30) REVERT: C 353 LYS cc_start: 0.7589 (mttt) cc_final: 0.7178 (tmtp) REVERT: D 331 LYS cc_start: 0.7713 (mttt) cc_final: 0.7218 (mmmt) REVERT: D 336 GLN cc_start: 0.8535 (tt0) cc_final: 0.8326 (tt0) REVERT: D 340 LYS cc_start: 0.8070 (tttt) cc_final: 0.7304 (tptt) REVERT: D 342 GLU cc_start: 0.7679 (tt0) cc_final: 0.7387 (tt0) REVERT: D 347 LYS cc_start: 0.7856 (mttt) cc_final: 0.7486 (mmtm) REVERT: D 349 ARG cc_start: 0.6417 (mtm180) cc_final: 0.4258 (pmt-80) REVERT: D 353 LYS cc_start: 0.7654 (mttt) cc_final: 0.7375 (tttm) REVERT: D 358 ASP cc_start: 0.7846 (m-30) cc_final: 0.7598 (m-30) REVERT: E 311 LYS cc_start: 0.6760 (mttt) cc_final: 0.5686 (mmtt) REVERT: E 338 GLU cc_start: 0.6683 (tt0) cc_final: 0.6004 (tp30) REVERT: E 345 ASP cc_start: 0.7525 (t0) cc_final: 0.7205 (m-30) REVERT: E 353 LYS cc_start: 0.6974 (mttt) cc_final: 0.6665 (tttm) REVERT: E 369 LYS cc_start: 0.7106 (tttt) cc_final: 0.6523 (ttmp) REVERT: F 311 LYS cc_start: 0.7287 (mttt) cc_final: 0.6020 (mmtt) REVERT: F 338 GLU cc_start: 0.7409 (tt0) cc_final: 0.7026 (tm-30) REVERT: F 340 LYS cc_start: 0.7381 (tttt) cc_final: 0.6549 (tptt) REVERT: F 349 ARG cc_start: 0.5764 (mtm180) cc_final: 0.5079 (mmp80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 3.7569 time to fit residues: 474.4595 Evaluate side-chains 82 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.7536 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3498 Z= 0.334 Angle : 0.563 4.766 4680 Z= 0.300 Chirality : 0.049 0.126 528 Planarity : 0.005 0.039 594 Dihedral : 5.524 13.297 462 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.01 % Allowed : 12.12 % Favored : 86.87 % 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 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 329 PHE 0.011 0.003 PHE E 346 TYR 0.006 0.001 TYR E 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7332 (mttt) cc_final: 0.6535 (mtpt) REVERT: A 338 GLU cc_start: 0.6849 (tt0) cc_final: 0.6047 (tp30) REVERT: A 345 ASP cc_start: 0.7610 (t0) cc_final: 0.7286 (m-30) REVERT: A 347 LYS cc_start: 0.8072 (mttt) cc_final: 0.7860 (mptp) REVERT: A 353 LYS cc_start: 0.6902 (mttt) cc_final: 0.6679 (tmtp) REVERT: A 369 LYS cc_start: 0.6975 (tttt) cc_final: 0.6360 (ttmt) REVERT: B 336 GLN cc_start: 0.8012 (tt0) cc_final: 0.7771 (tt0) REVERT: B 340 LYS cc_start: 0.7247 (tttt) cc_final: 0.6362 (tmtm) REVERT: B 353 LYS cc_start: 0.6959 (mttt) cc_final: 0.6743 (tttm) REVERT: C 317 LYS cc_start: 0.7864 (mttt) cc_final: 0.7398 (mtpt) REVERT: C 338 GLU cc_start: 0.7475 (tt0) cc_final: 0.6725 (tp30) REVERT: C 340 LYS cc_start: 0.7759 (tttt) cc_final: 0.7429 (ttpp) REVERT: C 349 ARG cc_start: 0.6378 (mtm-85) cc_final: 0.4805 (mtt90) REVERT: C 351 GLN cc_start: 0.8115 (tt0) cc_final: 0.7704 (tt0) REVERT: C 353 LYS cc_start: 0.7484 (mttt) cc_final: 0.7124 (tmtp) REVERT: D 340 LYS cc_start: 0.8006 (tttt) cc_final: 0.7205 (tptt) REVERT: D 347 LYS cc_start: 0.8002 (mttt) cc_final: 0.7690 (mmtm) REVERT: D 349 ARG cc_start: 0.6563 (mtm180) cc_final: 0.4545 (pmt-80) REVERT: D 353 LYS cc_start: 0.7634 (mttt) cc_final: 0.7410 (tttm) REVERT: E 311 LYS cc_start: 0.6946 (mttt) cc_final: 0.5732 (mmtt) REVERT: E 338 GLU cc_start: 0.6739 (tt0) cc_final: 0.6039 (tp30) REVERT: E 340 LYS cc_start: 0.7200 (tttt) cc_final: 0.6861 (ttpp) REVERT: E 345 ASP cc_start: 0.7594 (t0) cc_final: 0.7298 (m-30) REVERT: E 353 LYS cc_start: 0.7072 (mttt) cc_final: 0.6739 (tmtp) REVERT: E 369 LYS cc_start: 0.7132 (tttt) cc_final: 0.6573 (ttmp) REVERT: F 340 LYS cc_start: 0.7320 (tttt) cc_final: 0.6463 (tptt) REVERT: F 349 ARG cc_start: 0.5900 (mtm180) cc_final: 0.5008 (mmp80) outliers start: 4 outliers final: 0 residues processed: 88 average time/residue: 3.7617 time to fit residues: 337.2753 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.7530 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.137 Angle : 0.462 4.329 4680 Z= 0.234 Chirality : 0.050 0.129 528 Planarity : 0.003 0.031 594 Dihedral : 4.639 11.150 462 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.51 % Allowed : 15.15 % Favored : 84.34 % 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: -1.57 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.005 0.001 PHE B 378 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6350 (mt) cc_final: 0.6023 (mp) REVERT: A 317 LYS cc_start: 0.7302 (mttt) cc_final: 0.6500 (mtpt) REVERT: A 338 GLU cc_start: 0.6862 (tt0) cc_final: 0.6063 (tp30) REVERT: A 345 ASP cc_start: 0.7655 (t0) cc_final: 0.7316 (m-30) REVERT: A 347 LYS cc_start: 0.8059 (mttt) cc_final: 0.7848 (mptp) REVERT: A 351 GLN cc_start: 0.7371 (tt0) cc_final: 0.6885 (tt0) REVERT: A 353 LYS cc_start: 0.6893 (mttt) cc_final: 0.6662 (tmtp) REVERT: A 369 LYS cc_start: 0.6962 (tttt) cc_final: 0.6330 (ttmp) REVERT: B 307 GLN cc_start: 0.7390 (tt0) cc_final: 0.7186 (tm-30) REVERT: B 336 GLN cc_start: 0.7985 (tt0) cc_final: 0.7772 (tt0) REVERT: B 340 LYS cc_start: 0.7189 (tttt) cc_final: 0.6330 (tmtm) REVERT: B 353 LYS cc_start: 0.7038 (mttt) cc_final: 0.6818 (tttm) REVERT: C 317 LYS cc_start: 0.7807 (mttt) cc_final: 0.7291 (mtpt) REVERT: C 338 GLU cc_start: 0.7350 (tt0) cc_final: 0.6658 (tp30) REVERT: C 340 LYS cc_start: 0.7735 (tttt) cc_final: 0.7433 (ttpp) REVERT: C 349 ARG cc_start: 0.6290 (mtm-85) cc_final: 0.4860 (mtt90) REVERT: C 351 GLN cc_start: 0.8089 (tt0) cc_final: 0.7695 (tt0) REVERT: C 353 LYS cc_start: 0.7479 (mttt) cc_final: 0.7100 (tmtp) REVERT: D 340 LYS cc_start: 0.7909 (tttt) cc_final: 0.7161 (tptt) REVERT: D 347 LYS cc_start: 0.7978 (mttt) cc_final: 0.7678 (mmtm) REVERT: D 349 ARG cc_start: 0.6883 (mtm180) cc_final: 0.4381 (pmt-80) REVERT: D 353 LYS cc_start: 0.7686 (mttt) cc_final: 0.7398 (tttm) REVERT: E 338 GLU cc_start: 0.6768 (tt0) cc_final: 0.6052 (tp30) REVERT: E 340 LYS cc_start: 0.7099 (tttt) cc_final: 0.6797 (ttpp) REVERT: E 345 ASP cc_start: 0.7616 (t0) cc_final: 0.7248 (m-30) REVERT: E 351 GLN cc_start: 0.7374 (tt0) cc_final: 0.6981 (tt0) REVERT: E 353 LYS cc_start: 0.7093 (mttt) cc_final: 0.6768 (tmtp) REVERT: E 369 LYS cc_start: 0.7055 (tttt) cc_final: 0.6490 (ttmp) REVERT: F 340 LYS cc_start: 0.7224 (tttt) cc_final: 0.6374 (tptt) REVERT: F 349 ARG cc_start: 0.6021 (mtm180) cc_final: 0.5044 (mmp80) outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 3.7694 time to fit residues: 303.5648 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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: 0.7542 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.158 Angle : 0.444 4.208 4680 Z= 0.224 Chirality : 0.049 0.124 528 Planarity : 0.003 0.024 594 Dihedral : 4.447 10.772 462 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 15.91 % Favored : 83.08 % 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: -1.46 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.006 0.001 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6313 (mt) cc_final: 0.6011 (mp) REVERT: A 317 LYS cc_start: 0.7325 (mttt) cc_final: 0.6547 (mtpt) REVERT: A 338 GLU cc_start: 0.6897 (tt0) cc_final: 0.6103 (tp30) REVERT: A 345 ASP cc_start: 0.7642 (t0) cc_final: 0.7310 (m-30) REVERT: A 351 GLN cc_start: 0.7401 (tt0) cc_final: 0.6897 (tt0) REVERT: A 353 LYS cc_start: 0.6886 (mttt) cc_final: 0.6664 (tmtp) REVERT: B 336 GLN cc_start: 0.8017 (tt0) cc_final: 0.7794 (tt0) REVERT: B 340 LYS cc_start: 0.7185 (tttt) cc_final: 0.6335 (tmtm) REVERT: B 353 LYS cc_start: 0.6986 (mttt) cc_final: 0.6760 (tttm) REVERT: C 317 LYS cc_start: 0.7855 (mttt) cc_final: 0.7266 (mtpt) REVERT: C 338 GLU cc_start: 0.7331 (tt0) cc_final: 0.6649 (tp30) REVERT: C 340 LYS cc_start: 0.7737 (tttt) cc_final: 0.7438 (ttpp) REVERT: C 347 LYS cc_start: 0.8606 (mppt) cc_final: 0.8210 (mptp) REVERT: C 349 ARG cc_start: 0.6281 (mtm-85) cc_final: 0.4862 (mtt90) REVERT: C 351 GLN cc_start: 0.8096 (tt0) cc_final: 0.7710 (tt0) REVERT: C 353 LYS cc_start: 0.7513 (mttt) cc_final: 0.7114 (tmtp) REVERT: D 340 LYS cc_start: 0.7913 (tttt) cc_final: 0.7162 (tptt) REVERT: D 347 LYS cc_start: 0.7958 (mttt) cc_final: 0.7679 (mmtm) REVERT: D 349 ARG cc_start: 0.6967 (mtm180) cc_final: 0.4513 (pmt-80) REVERT: D 353 LYS cc_start: 0.7684 (mttt) cc_final: 0.7409 (tttm) REVERT: E 317 LYS cc_start: 0.7455 (mttt) cc_final: 0.6373 (ttmm) REVERT: E 338 GLU cc_start: 0.6744 (tt0) cc_final: 0.6039 (tp30) REVERT: E 340 LYS cc_start: 0.7082 (tttt) cc_final: 0.6796 (ttpp) REVERT: E 345 ASP cc_start: 0.7671 (t0) cc_final: 0.7234 (m-30) REVERT: E 351 GLN cc_start: 0.7397 (tt0) cc_final: 0.6999 (tt0) REVERT: E 353 LYS cc_start: 0.7131 (mttt) cc_final: 0.6718 (tmtp) REVERT: E 369 LYS cc_start: 0.7063 (tttt) cc_final: 0.6456 (ttmp) REVERT: F 340 LYS cc_start: 0.7214 (tttt) cc_final: 0.6352 (tptt) REVERT: F 349 ARG cc_start: 0.6052 (mtm180) cc_final: 0.5005 (mmp80) outliers start: 4 outliers final: 1 residues processed: 81 average time/residue: 3.6961 time to fit residues: 305.2711 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 overall best weight: 2.3524 ------------------------------------------------------------------------------- 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: 0.7556 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.181 Angle : 0.445 4.302 4680 Z= 0.226 Chirality : 0.049 0.123 528 Planarity : 0.003 0.024 594 Dihedral : 4.457 11.794 462 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 15.40 % Favored : 83.08 % 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: -1.55 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.007 0.001 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6318 (mt) cc_final: 0.6006 (mp) REVERT: A 317 LYS cc_start: 0.7320 (mttt) cc_final: 0.6438 (mtpt) REVERT: A 338 GLU cc_start: 0.6946 (tt0) cc_final: 0.6149 (tp30) REVERT: A 345 ASP cc_start: 0.7699 (t0) cc_final: 0.7304 (m-30) REVERT: A 351 GLN cc_start: 0.7434 (tt0) cc_final: 0.6985 (tt0) REVERT: A 353 LYS cc_start: 0.6933 (mttt) cc_final: 0.6665 (tmtp) REVERT: A 358 ASP cc_start: 0.7474 (m-30) cc_final: 0.7267 (m-30) REVERT: B 336 GLN cc_start: 0.8012 (tt0) cc_final: 0.7791 (tt0) REVERT: B 340 LYS cc_start: 0.7210 (tttt) cc_final: 0.6362 (tmtm) REVERT: B 353 LYS cc_start: 0.6995 (mttt) cc_final: 0.6768 (tttm) REVERT: C 317 LYS cc_start: 0.7927 (mttt) cc_final: 0.7246 (mtpt) REVERT: C 338 GLU cc_start: 0.7350 (tt0) cc_final: 0.6674 (tp30) REVERT: C 340 LYS cc_start: 0.7748 (tttt) cc_final: 0.7449 (ttpp) REVERT: C 347 LYS cc_start: 0.8607 (mppt) cc_final: 0.8212 (mptp) REVERT: C 349 ARG cc_start: 0.6259 (mtm-85) cc_final: 0.4852 (mtt90) REVERT: C 353 LYS cc_start: 0.7473 (mttt) cc_final: 0.7103 (tmtp) REVERT: D 340 LYS cc_start: 0.7926 (tttt) cc_final: 0.7168 (tptt) REVERT: D 347 LYS cc_start: 0.7945 (mttt) cc_final: 0.7656 (mmtm) REVERT: D 349 ARG cc_start: 0.7004 (mtm180) cc_final: 0.4515 (pmt-80) REVERT: D 353 LYS cc_start: 0.7629 (mttt) cc_final: 0.7388 (tttm) REVERT: E 317 LYS cc_start: 0.7375 (mttt) cc_final: 0.6296 (ttmm) REVERT: E 338 GLU cc_start: 0.6736 (tt0) cc_final: 0.6077 (tp30) REVERT: E 340 LYS cc_start: 0.7075 (tttt) cc_final: 0.6781 (ttpp) REVERT: E 345 ASP cc_start: 0.7714 (t0) cc_final: 0.7199 (m-30) REVERT: E 351 GLN cc_start: 0.7395 (tt0) cc_final: 0.7052 (tt0) REVERT: E 353 LYS cc_start: 0.7127 (mttt) cc_final: 0.6721 (tmtp) REVERT: E 369 LYS cc_start: 0.7048 (tttt) cc_final: 0.6479 (ttmp) REVERT: F 340 LYS cc_start: 0.7233 (tttt) cc_final: 0.6375 (tptt) REVERT: F 349 ARG cc_start: 0.6068 (mtm180) cc_final: 0.4924 (mmp80) outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 3.5968 time to fit residues: 297.1389 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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: 0.7570 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.221 Angle : 0.459 4.359 4680 Z= 0.233 Chirality : 0.049 0.122 528 Planarity : 0.003 0.024 594 Dihedral : 4.536 11.895 462 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.26 % Allowed : 16.67 % Favored : 82.07 % 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: -1.70 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.008 0.002 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6357 (mt) cc_final: 0.6029 (mp) REVERT: A 317 LYS cc_start: 0.7369 (mttt) cc_final: 0.6472 (mtpt) REVERT: A 338 GLU cc_start: 0.6916 (tt0) cc_final: 0.6142 (tp30) REVERT: A 345 ASP cc_start: 0.7759 (t0) cc_final: 0.7280 (m-30) REVERT: A 351 GLN cc_start: 0.7461 (tt0) cc_final: 0.7021 (tt0) REVERT: A 353 LYS cc_start: 0.6969 (mttt) cc_final: 0.6680 (tmtp) REVERT: B 336 GLN cc_start: 0.8002 (tt0) cc_final: 0.7783 (tt0) REVERT: B 340 LYS cc_start: 0.7249 (tttt) cc_final: 0.6401 (tmtm) REVERT: B 353 LYS cc_start: 0.6996 (mttt) cc_final: 0.6776 (tttp) REVERT: C 317 LYS cc_start: 0.7899 (mttt) cc_final: 0.7224 (mtpt) REVERT: C 338 GLU cc_start: 0.7363 (tt0) cc_final: 0.6683 (tp30) REVERT: C 340 LYS cc_start: 0.7755 (tttt) cc_final: 0.7446 (ttpp) REVERT: C 347 LYS cc_start: 0.8636 (mppt) cc_final: 0.8234 (mptp) REVERT: C 349 ARG cc_start: 0.6294 (mtm-85) cc_final: 0.4942 (mtt90) REVERT: C 353 LYS cc_start: 0.7508 (mttt) cc_final: 0.7136 (tmtp) REVERT: D 340 LYS cc_start: 0.7937 (tttt) cc_final: 0.7165 (tptt) REVERT: D 347 LYS cc_start: 0.7941 (mttt) cc_final: 0.7654 (mmtm) REVERT: D 353 LYS cc_start: 0.7595 (mttt) cc_final: 0.7390 (tttm) REVERT: E 338 GLU cc_start: 0.6791 (tt0) cc_final: 0.6094 (tp30) REVERT: E 340 LYS cc_start: 0.7083 (tttt) cc_final: 0.6776 (ttpp) REVERT: E 345 ASP cc_start: 0.7699 (t0) cc_final: 0.7147 (m-30) REVERT: E 351 GLN cc_start: 0.7474 (tt0) cc_final: 0.7065 (tt0) REVERT: E 353 LYS cc_start: 0.7135 (mttt) cc_final: 0.6737 (tmtp) REVERT: E 369 LYS cc_start: 0.7056 (tttt) cc_final: 0.6460 (ttmt) REVERT: F 340 LYS cc_start: 0.7217 (tttt) cc_final: 0.6383 (tptt) REVERT: F 349 ARG cc_start: 0.6123 (mtm180) cc_final: 0.4955 (mmp80) outliers start: 5 outliers final: 2 residues processed: 79 average time/residue: 3.5437 time to fit residues: 285.5823 Evaluate side-chains 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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: 0.7560 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3498 Z= 0.153 Angle : 0.431 4.224 4680 Z= 0.217 Chirality : 0.049 0.125 528 Planarity : 0.003 0.022 594 Dihedral : 4.284 11.292 462 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.77 % Allowed : 16.67 % Favored : 81.57 % 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: -1.64 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.005 0.001 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6362 (mt) cc_final: 0.6043 (mp) REVERT: A 317 LYS cc_start: 0.7358 (mttt) cc_final: 0.6464 (mtpt) REVERT: A 338 GLU cc_start: 0.6981 (tt0) cc_final: 0.6203 (tp30) REVERT: A 345 ASP cc_start: 0.7703 (t0) cc_final: 0.7269 (m-30) REVERT: A 351 GLN cc_start: 0.7419 (tt0) cc_final: 0.6984 (tt0) REVERT: A 353 LYS cc_start: 0.6953 (mttt) cc_final: 0.6687 (tmtp) REVERT: B 336 GLN cc_start: 0.8016 (tt0) cc_final: 0.7803 (tt0) REVERT: B 340 LYS cc_start: 0.7216 (tttt) cc_final: 0.6367 (tmtm) REVERT: B 353 LYS cc_start: 0.6964 (mttt) cc_final: 0.6752 (tttm) REVERT: C 317 LYS cc_start: 0.7822 (mttt) cc_final: 0.7165 (mtpt) REVERT: C 338 GLU cc_start: 0.7339 (tt0) cc_final: 0.6640 (tp30) REVERT: C 340 LYS cc_start: 0.7741 (tttt) cc_final: 0.7440 (ttpp) REVERT: C 347 LYS cc_start: 0.8630 (mppt) cc_final: 0.8235 (mptp) REVERT: C 349 ARG cc_start: 0.6343 (mtm-85) cc_final: 0.4987 (mtt90) REVERT: C 353 LYS cc_start: 0.7521 (mttt) cc_final: 0.7133 (tmtp) REVERT: D 340 LYS cc_start: 0.7942 (tttt) cc_final: 0.7175 (tptt) REVERT: D 347 LYS cc_start: 0.7994 (mttt) cc_final: 0.7704 (mmtm) REVERT: E 338 GLU cc_start: 0.6752 (tt0) cc_final: 0.6067 (tp30) REVERT: E 340 LYS cc_start: 0.7039 (tttt) cc_final: 0.6758 (ttpp) REVERT: E 345 ASP cc_start: 0.7706 (t0) cc_final: 0.7178 (m-30) REVERT: E 351 GLN cc_start: 0.7424 (tt0) cc_final: 0.7068 (tt0) REVERT: E 353 LYS cc_start: 0.7129 (mttt) cc_final: 0.6748 (tmtp) REVERT: E 369 LYS cc_start: 0.7020 (tttt) cc_final: 0.6447 (ttmp) REVERT: F 340 LYS cc_start: 0.7191 (tttt) cc_final: 0.6364 (tptt) REVERT: F 349 ARG cc_start: 0.6184 (mtm180) cc_final: 0.4998 (mmp80) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 3.7305 time to fit residues: 312.5989 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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: 0.7582 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.261 Angle : 0.475 4.406 4680 Z= 0.242 Chirality : 0.049 0.122 528 Planarity : 0.003 0.025 594 Dihedral : 4.574 12.394 462 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.77 % Allowed : 17.42 % 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 (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: -1.84 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.009 0.002 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6417 (mt) cc_final: 0.6078 (mp) REVERT: A 317 LYS cc_start: 0.7380 (mttt) cc_final: 0.6465 (mtpt) REVERT: A 338 GLU cc_start: 0.6864 (tt0) cc_final: 0.6093 (tp30) REVERT: A 340 LYS cc_start: 0.7195 (tttt) cc_final: 0.6811 (ttpp) REVERT: A 345 ASP cc_start: 0.7774 (t0) cc_final: 0.7304 (m-30) REVERT: A 351 GLN cc_start: 0.7459 (tt0) cc_final: 0.7035 (tt0) REVERT: A 353 LYS cc_start: 0.6955 (mttt) cc_final: 0.6658 (tmtp) REVERT: B 336 GLN cc_start: 0.8005 (tt0) cc_final: 0.7795 (tt0) REVERT: B 340 LYS cc_start: 0.7235 (tttt) cc_final: 0.6376 (tmtm) REVERT: B 349 ARG cc_start: 0.6712 (mtm110) cc_final: 0.6178 (mtt90) REVERT: C 317 LYS cc_start: 0.7852 (mttt) cc_final: 0.7105 (mtpt) REVERT: C 338 GLU cc_start: 0.7377 (tt0) cc_final: 0.6685 (tp30) REVERT: C 340 LYS cc_start: 0.7787 (tttt) cc_final: 0.7456 (ttpp) REVERT: C 347 LYS cc_start: 0.8634 (mppt) cc_final: 0.8228 (mptp) REVERT: C 349 ARG cc_start: 0.6365 (mtm-85) cc_final: 0.5016 (mtt90) REVERT: C 353 LYS cc_start: 0.7510 (mttt) cc_final: 0.7151 (tmtp) REVERT: D 340 LYS cc_start: 0.7943 (tttt) cc_final: 0.7165 (tptt) REVERT: D 347 LYS cc_start: 0.7957 (mttt) cc_final: 0.7642 (mmtm) REVERT: D 349 ARG cc_start: 0.6578 (mtm-85) cc_final: 0.3946 (pmt-80) REVERT: E 338 GLU cc_start: 0.6807 (tt0) cc_final: 0.6094 (tp30) REVERT: E 340 LYS cc_start: 0.7066 (tttt) cc_final: 0.6739 (ttpp) REVERT: E 345 ASP cc_start: 0.7721 (t0) cc_final: 0.7152 (m-30) REVERT: E 351 GLN cc_start: 0.7489 (tt0) cc_final: 0.7131 (tt0) REVERT: E 353 LYS cc_start: 0.7138 (mttt) cc_final: 0.6735 (tmtp) REVERT: E 369 LYS cc_start: 0.7081 (tttt) cc_final: 0.6451 (ttmt) REVERT: F 340 LYS cc_start: 0.7216 (tttt) cc_final: 0.6333 (tptt) REVERT: F 349 ARG cc_start: 0.6233 (mtm180) cc_final: 0.4966 (mmp80) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 3.5214 time to fit residues: 280.2261 Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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: 0.7583 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.254 Angle : 0.469 4.437 4680 Z= 0.239 Chirality : 0.049 0.121 528 Planarity : 0.003 0.025 594 Dihedral : 4.553 12.503 462 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.26 % Allowed : 18.43 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.008 0.002 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6430 (mt) cc_final: 0.6090 (mp) REVERT: A 317 LYS cc_start: 0.7392 (mttt) cc_final: 0.6503 (mtpt) REVERT: A 338 GLU cc_start: 0.6896 (tt0) cc_final: 0.6131 (tp30) REVERT: A 345 ASP cc_start: 0.7765 (t0) cc_final: 0.7303 (m-30) REVERT: A 351 GLN cc_start: 0.7472 (tt0) cc_final: 0.7043 (tt0) REVERT: A 353 LYS cc_start: 0.6933 (mttt) cc_final: 0.6643 (tmtp) REVERT: B 336 GLN cc_start: 0.8004 (tt0) cc_final: 0.7785 (tt0) REVERT: B 340 LYS cc_start: 0.7248 (tttt) cc_final: 0.6376 (tmtm) REVERT: C 338 GLU cc_start: 0.7391 (tt0) cc_final: 0.6701 (tp30) REVERT: C 340 LYS cc_start: 0.7756 (tttt) cc_final: 0.7440 (ttpp) REVERT: C 347 LYS cc_start: 0.8631 (mppt) cc_final: 0.8227 (mptp) REVERT: C 349 ARG cc_start: 0.6343 (mtm-85) cc_final: 0.5020 (mtt90) REVERT: C 353 LYS cc_start: 0.7539 (mttt) cc_final: 0.7172 (tmtp) REVERT: D 340 LYS cc_start: 0.7938 (tttt) cc_final: 0.7161 (tptt) REVERT: D 347 LYS cc_start: 0.7968 (mttt) cc_final: 0.7650 (mmtm) REVERT: D 349 ARG cc_start: 0.6597 (mtm-85) cc_final: 0.3967 (pmt-80) REVERT: E 338 GLU cc_start: 0.6832 (tt0) cc_final: 0.6139 (tp30) REVERT: E 340 LYS cc_start: 0.7076 (tttt) cc_final: 0.6758 (ttpp) REVERT: E 345 ASP cc_start: 0.7721 (t0) cc_final: 0.7159 (m-30) REVERT: E 351 GLN cc_start: 0.7487 (tt0) cc_final: 0.7135 (tt0) REVERT: E 353 LYS cc_start: 0.7153 (mttt) cc_final: 0.6755 (tmtp) REVERT: F 340 LYS cc_start: 0.7204 (tttt) cc_final: 0.6325 (tptt) REVERT: F 345 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7797 (t0) REVERT: F 349 ARG cc_start: 0.6284 (mtm180) cc_final: 0.4934 (mmp80) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 3.5054 time to fit residues: 275.4714 Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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: 0.7589 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.222 Angle : 0.460 4.400 4680 Z= 0.233 Chirality : 0.049 0.122 528 Planarity : 0.003 0.025 594 Dihedral : 4.453 12.327 462 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 19.19 % Favored : 79.80 % 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: -1.94 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 374 PHE 0.007 0.001 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.002 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.591 Fit side-chains REVERT: A 308 ILE cc_start: 0.6416 (mt) cc_final: 0.6078 (mp) REVERT: A 338 GLU cc_start: 0.6920 (tt0) cc_final: 0.6158 (tp30) REVERT: A 340 LYS cc_start: 0.7179 (tttt) cc_final: 0.6807 (ttpp) REVERT: A 345 ASP cc_start: 0.7758 (t0) cc_final: 0.7286 (m-30) REVERT: A 351 GLN cc_start: 0.7463 (tt0) cc_final: 0.7030 (tt0) REVERT: A 353 LYS cc_start: 0.6935 (mttt) cc_final: 0.6660 (tmtp) REVERT: B 336 GLN cc_start: 0.8003 (tt0) cc_final: 0.7784 (tt0) REVERT: B 340 LYS cc_start: 0.7239 (tttt) cc_final: 0.6375 (tmtm) REVERT: C 338 GLU cc_start: 0.7368 (tt0) cc_final: 0.6660 (tp30) REVERT: C 340 LYS cc_start: 0.7747 (tttt) cc_final: 0.7430 (ttpp) REVERT: C 347 LYS cc_start: 0.8630 (mppt) cc_final: 0.8223 (mptp) REVERT: C 349 ARG cc_start: 0.6470 (mtm-85) cc_final: 0.5170 (mtt90) REVERT: C 353 LYS cc_start: 0.7511 (mttt) cc_final: 0.7169 (tmtp) REVERT: D 340 LYS cc_start: 0.7937 (tttt) cc_final: 0.7164 (tptt) REVERT: D 347 LYS cc_start: 0.7949 (mttt) cc_final: 0.7631 (mmtm) REVERT: D 349 ARG cc_start: 0.6560 (mtm-85) cc_final: 0.3945 (pmt-80) REVERT: E 338 GLU cc_start: 0.6823 (tt0) cc_final: 0.6130 (tp30) REVERT: E 340 LYS cc_start: 0.7082 (tttt) cc_final: 0.6750 (ttpp) REVERT: E 345 ASP cc_start: 0.7714 (t0) cc_final: 0.7197 (m-30) REVERT: E 351 GLN cc_start: 0.7456 (tt0) cc_final: 0.7064 (tt0) REVERT: E 353 LYS cc_start: 0.7133 (mttt) cc_final: 0.6739 (tmtp) REVERT: F 340 LYS cc_start: 0.7185 (tttt) cc_final: 0.6304 (tptt) REVERT: F 349 ARG cc_start: 0.6318 (mtm180) cc_final: 0.4953 (mmp80) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 3.5374 time to fit residues: 252.8941 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.136809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128321 restraints weight = 14521.762| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.36 r_work: 0.3777 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.139 Angle : 0.430 4.188 4680 Z= 0.215 Chirality : 0.050 0.123 528 Planarity : 0.003 0.023 594 Dihedral : 4.115 11.413 462 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 19.70 % Favored : 79.55 % 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: -1.78 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 330 PHE 0.004 0.001 PHE A 378 TYR 0.004 0.001 TYR E 310 ARG 0.002 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5359.37 seconds wall clock time: 93 minutes 56.30 seconds (5636.30 seconds total)