Starting phenix.real_space_refine on Thu Jan 18 00:26:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/01_2024/8q2k_18111.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/01_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_18111/01_2024/8q2k_18111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/01_2024/8q2k_18111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/01_2024/8q2k_18111.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2k_18111/01_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-1.21-5211/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: 3.44, per 1000 atoms: 0.49 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: 5.32 Conformation dependent library (CDL) restraints added in 736.8 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: 0.69 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: 2.30 Time building geometry restraints manager: 5.57 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: 2878 15.15 - 30.31: 150 30.31 - 45.46: 42 45.46 - 60.61: 40 60.61 - 75.76: 46 Dihedral angle restraints: 3156 sinusoidal: 1758 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 3153 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: 2.280 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: 11.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.940 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.410 ------------------------------------------------------------------------------- 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 : 0.595 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: 3.5899 time to fit residues: 453.1963 Evaluate side-chains 82 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.7533 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3498 Z= 0.347 Angle : 0.553 4.787 4680 Z= 0.292 Chirality : 0.049 0.125 528 Planarity : 0.005 0.039 594 Dihedral : 5.511 13.204 462 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.01 % Allowed : 11.87 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.009 0.002 PHE E 346 TYR 0.005 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 91 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7337 (mttt) cc_final: 0.6536 (mtpt) REVERT: A 338 GLU cc_start: 0.6849 (tt0) cc_final: 0.6049 (tp30) REVERT: A 345 ASP cc_start: 0.7584 (t0) cc_final: 0.7279 (m-30) REVERT: A 347 LYS cc_start: 0.8067 (mttt) cc_final: 0.7856 (mptp) REVERT: A 353 LYS cc_start: 0.6880 (mttt) cc_final: 0.6653 (tmtp) REVERT: A 369 LYS cc_start: 0.7002 (tttt) cc_final: 0.6390 (ttmt) REVERT: B 336 GLN cc_start: 0.8009 (tt0) cc_final: 0.7767 (tt0) REVERT: B 340 LYS cc_start: 0.7214 (tttt) cc_final: 0.6356 (tmtm) REVERT: B 353 LYS cc_start: 0.7003 (mttt) cc_final: 0.6788 (tttm) REVERT: C 317 LYS cc_start: 0.7861 (mttt) cc_final: 0.7396 (mtpt) REVERT: C 338 GLU cc_start: 0.7470 (tt0) cc_final: 0.6724 (tp30) REVERT: C 340 LYS cc_start: 0.7752 (tttt) cc_final: 0.7425 (ttpp) REVERT: C 349 ARG cc_start: 0.6375 (mtm-85) cc_final: 0.4815 (mtt90) REVERT: C 351 GLN cc_start: 0.8128 (tt0) cc_final: 0.7716 (tt0) REVERT: C 353 LYS cc_start: 0.7481 (mttt) cc_final: 0.7115 (tmtp) REVERT: D 340 LYS cc_start: 0.8003 (tttt) cc_final: 0.7216 (tptt) REVERT: D 347 LYS cc_start: 0.8006 (mttt) cc_final: 0.7693 (mmtm) REVERT: D 349 ARG cc_start: 0.6575 (mtm180) cc_final: 0.4547 (pmt-80) REVERT: D 353 LYS cc_start: 0.7626 (mttt) cc_final: 0.7407 (tttm) REVERT: E 311 LYS cc_start: 0.6952 (mttt) cc_final: 0.5745 (mmtt) REVERT: E 338 GLU cc_start: 0.6734 (tt0) cc_final: 0.6026 (tp30) REVERT: E 340 LYS cc_start: 0.7189 (tttt) cc_final: 0.6853 (ttpp) REVERT: E 345 ASP cc_start: 0.7605 (t0) cc_final: 0.7285 (m-30) REVERT: E 353 LYS cc_start: 0.7045 (mttt) cc_final: 0.6722 (tmtp) REVERT: E 369 LYS cc_start: 0.7128 (tttt) cc_final: 0.6571 (ttmp) REVERT: F 340 LYS cc_start: 0.7308 (tttt) cc_final: 0.6465 (tptt) REVERT: F 349 ARG cc_start: 0.5899 (mtm180) cc_final: 0.5006 (mmp80) outliers start: 4 outliers final: 0 residues processed: 89 average time/residue: 3.6176 time to fit residues: 328.0411 Evaluate side-chains 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.7546 moved from start: 0.3779 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= 0.174 Angle : 0.475 4.352 4680 Z= 0.242 Chirality : 0.050 0.130 528 Planarity : 0.004 0.032 594 Dihedral : 4.756 11.559 462 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 15.66 % Favored : 83.33 % 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: -1.71 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.006 0.002 PHE F 378 TYR 0.005 0.001 TYR E 310 ARG 0.002 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 86 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6355 (mt) cc_final: 0.6022 (mp) REVERT: A 317 LYS cc_start: 0.7352 (mttt) cc_final: 0.6485 (mtpt) REVERT: A 338 GLU cc_start: 0.6900 (tt0) cc_final: 0.6085 (tp30) REVERT: A 345 ASP cc_start: 0.7667 (t0) cc_final: 0.7316 (m-30) REVERT: A 351 GLN cc_start: 0.7406 (tt0) cc_final: 0.6872 (tt0) REVERT: A 353 LYS cc_start: 0.6883 (mttt) cc_final: 0.6662 (tmtp) REVERT: A 369 LYS cc_start: 0.6962 (tttt) cc_final: 0.6317 (ttmp) REVERT: B 307 GLN cc_start: 0.7380 (tt0) cc_final: 0.7150 (tm-30) REVERT: B 336 GLN cc_start: 0.8011 (tt0) cc_final: 0.7799 (tt0) REVERT: B 340 LYS cc_start: 0.7213 (tttt) cc_final: 0.6333 (tmtm) REVERT: C 317 LYS cc_start: 0.7887 (mttt) cc_final: 0.7309 (mtpt) REVERT: C 338 GLU cc_start: 0.7381 (tt0) cc_final: 0.6674 (tp30) REVERT: C 340 LYS cc_start: 0.7750 (tttt) cc_final: 0.7440 (ttpp) REVERT: C 347 LYS cc_start: 0.8607 (mppt) cc_final: 0.8209 (mptp) REVERT: C 349 ARG cc_start: 0.6294 (mtm-85) cc_final: 0.4891 (mtt90) REVERT: C 351 GLN cc_start: 0.8118 (tt0) cc_final: 0.7700 (tt0) REVERT: C 353 LYS cc_start: 0.7475 (mttt) cc_final: 0.7094 (tmtp) REVERT: D 340 LYS cc_start: 0.7919 (tttt) cc_final: 0.7170 (tptt) REVERT: D 347 LYS cc_start: 0.7957 (mttt) cc_final: 0.7670 (mmtm) REVERT: D 349 ARG cc_start: 0.6969 (mtm180) cc_final: 0.4524 (pmt-80) REVERT: D 353 LYS cc_start: 0.7709 (mttt) cc_final: 0.7437 (tttm) REVERT: E 317 LYS cc_start: 0.7430 (mttt) cc_final: 0.6390 (ttmm) REVERT: E 338 GLU cc_start: 0.6760 (tt0) cc_final: 0.6039 (tp30) REVERT: E 340 LYS cc_start: 0.7124 (tttt) cc_final: 0.6805 (ttpp) REVERT: E 345 ASP cc_start: 0.7673 (t0) cc_final: 0.7227 (m-30) REVERT: E 351 GLN cc_start: 0.7402 (tt0) cc_final: 0.7008 (tt0) REVERT: E 353 LYS cc_start: 0.7105 (mttt) cc_final: 0.6733 (tmtp) REVERT: E 369 LYS cc_start: 0.7061 (tttt) cc_final: 0.6485 (ttmp) REVERT: F 340 LYS cc_start: 0.7247 (tttt) cc_final: 0.6395 (tptt) REVERT: F 349 ARG cc_start: 0.6018 (mtm180) cc_final: 0.4993 (mmp80) outliers start: 4 outliers final: 1 residues processed: 83 average time/residue: 3.6498 time to fit residues: 308.7710 Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 372 GLU 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: 2.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.7537 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.115 Angle : 0.427 4.138 4680 Z= 0.214 Chirality : 0.050 0.125 528 Planarity : 0.003 0.023 594 Dihedral : 4.312 10.737 462 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.26 % Allowed : 15.40 % Favored : 83.33 % 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: -1.45 (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 0.003 0.001 HIS E 330 PHE 0.003 0.001 PHE F 378 TYR 0.004 0.001 TYR E 310 ARG 0.001 0.000 ARG B 379 *********************** 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: 5 poor density : 79 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6400 (mt) cc_final: 0.6106 (mp) REVERT: A 317 LYS cc_start: 0.7318 (mttt) cc_final: 0.6467 (mtpt) REVERT: A 338 GLU cc_start: 0.6912 (tt0) cc_final: 0.6119 (tp30) REVERT: A 345 ASP cc_start: 0.7632 (t0) cc_final: 0.7302 (m-30) REVERT: A 351 GLN cc_start: 0.7337 (tt0) cc_final: 0.6878 (tt0) REVERT: A 353 LYS cc_start: 0.6920 (mttt) cc_final: 0.6667 (tmtp) REVERT: B 336 GLN cc_start: 0.8004 (tt0) cc_final: 0.7784 (tt0) REVERT: B 340 LYS cc_start: 0.7177 (tttt) cc_final: 0.6325 (tmtm) REVERT: C 317 LYS cc_start: 0.7861 (mttt) cc_final: 0.7261 (mtpt) REVERT: C 338 GLU cc_start: 0.7345 (tt0) cc_final: 0.6638 (tp30) REVERT: C 340 LYS cc_start: 0.7751 (tttt) cc_final: 0.7429 (ttpp) REVERT: C 347 LYS cc_start: 0.8602 (mppt) cc_final: 0.8204 (mptp) REVERT: C 351 GLN cc_start: 0.8075 (tt0) cc_final: 0.7677 (tt0) REVERT: C 353 LYS cc_start: 0.7501 (mttt) cc_final: 0.7104 (tmtp) REVERT: D 340 LYS cc_start: 0.7909 (tttt) cc_final: 0.7164 (tptt) REVERT: D 347 LYS cc_start: 0.8034 (mttt) cc_final: 0.7743 (mmtm) REVERT: E 317 LYS cc_start: 0.7407 (mttt) cc_final: 0.6338 (tttp) REVERT: E 338 GLU cc_start: 0.6728 (tt0) cc_final: 0.6017 (tp30) REVERT: E 340 LYS cc_start: 0.7068 (tttt) cc_final: 0.6782 (ttpp) REVERT: E 345 ASP cc_start: 0.7695 (t0) cc_final: 0.7221 (m-30) REVERT: E 351 GLN cc_start: 0.7361 (tt0) cc_final: 0.6910 (tt0) REVERT: E 353 LYS cc_start: 0.7151 (mttt) cc_final: 0.6737 (tmtp) REVERT: E 369 LYS cc_start: 0.7025 (tttt) cc_final: 0.6451 (ttmp) REVERT: F 340 LYS cc_start: 0.7188 (tttt) cc_final: 0.6343 (tptt) REVERT: F 349 ARG cc_start: 0.6072 (mtm180) cc_final: 0.5005 (mmp80) outliers start: 5 outliers final: 1 residues processed: 81 average time/residue: 3.5351 time to fit residues: 292.0776 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.7554 moved from start: 0.4194 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= 0.187 Angle : 0.447 4.268 4680 Z= 0.226 Chirality : 0.049 0.122 528 Planarity : 0.003 0.022 594 Dihedral : 4.430 11.526 462 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.26 % Allowed : 16.41 % Favored : 82.32 % 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 : -1.17 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.007 0.002 PHE A 378 TYR 0.006 0.001 TYR A 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 82 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6286 (mt) cc_final: 0.5974 (mp) REVERT: A 317 LYS cc_start: 0.7340 (mttt) cc_final: 0.6455 (mtpt) REVERT: A 338 GLU cc_start: 0.6935 (tt0) cc_final: 0.6118 (tp30) REVERT: A 345 ASP cc_start: 0.7716 (t0) cc_final: 0.7311 (m-30) REVERT: A 351 GLN cc_start: 0.7423 (tt0) cc_final: 0.6977 (tt0) REVERT: A 353 LYS cc_start: 0.6923 (mttt) cc_final: 0.6663 (tmtp) REVERT: A 372 GLU cc_start: 0.7243 (tt0) cc_final: 0.6931 (tt0) REVERT: B 336 GLN cc_start: 0.8012 (tt0) cc_final: 0.7801 (tt0) REVERT: B 340 LYS cc_start: 0.7213 (tttt) cc_final: 0.6366 (tmtm) REVERT: C 317 LYS cc_start: 0.7931 (mttt) cc_final: 0.7244 (mtpt) REVERT: C 338 GLU cc_start: 0.7348 (tt0) cc_final: 0.6653 (tp30) REVERT: C 340 LYS cc_start: 0.7746 (tttt) cc_final: 0.7445 (ttpp) REVERT: C 347 LYS cc_start: 0.8631 (mppt) cc_final: 0.8238 (mptp) REVERT: C 349 ARG cc_start: 0.6289 (mtm-85) cc_final: 0.4883 (mtt90) REVERT: C 353 LYS cc_start: 0.7471 (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: 0.8005 (mttt) cc_final: 0.7723 (mmtm) REVERT: D 349 ARG cc_start: 0.7015 (mtm180) cc_final: 0.4518 (pmt-80) REVERT: E 317 LYS cc_start: 0.7394 (mttt) cc_final: 0.6301 (ttmm) REVERT: E 338 GLU cc_start: 0.6732 (tt0) cc_final: 0.6022 (tp30) REVERT: E 340 LYS cc_start: 0.7076 (tttt) cc_final: 0.6778 (ttpp) REVERT: E 345 ASP cc_start: 0.7720 (t0) cc_final: 0.7197 (m-30) REVERT: E 351 GLN cc_start: 0.7420 (tt0) cc_final: 0.7053 (tt0) REVERT: E 353 LYS cc_start: 0.7138 (mttt) cc_final: 0.6721 (tmtp) REVERT: E 369 LYS cc_start: 0.7062 (tttt) cc_final: 0.6502 (ttmp) REVERT: F 340 LYS cc_start: 0.7244 (tttt) cc_final: 0.6386 (tptt) REVERT: F 349 ARG cc_start: 0.6080 (mtm180) cc_final: 0.4940 (mmp80) outliers start: 5 outliers final: 2 residues processed: 78 average time/residue: 3.6643 time to fit residues: 291.2917 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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: 0.7559 moved from start: 0.4315 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= 0.188 Angle : 0.443 4.340 4680 Z= 0.225 Chirality : 0.049 0.125 528 Planarity : 0.003 0.023 594 Dihedral : 4.444 12.272 462 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.26 % Allowed : 17.42 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 B 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 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 82 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6322 (mt) cc_final: 0.6000 (mp) REVERT: A 317 LYS cc_start: 0.7368 (mttt) cc_final: 0.6452 (mtpt) REVERT: A 338 GLU cc_start: 0.6928 (tt0) cc_final: 0.6141 (tp30) REVERT: A 345 ASP cc_start: 0.7758 (t0) cc_final: 0.7326 (m-30) REVERT: A 351 GLN cc_start: 0.7406 (tt0) cc_final: 0.6973 (tt0) REVERT: A 353 LYS cc_start: 0.6959 (mttt) cc_final: 0.6683 (tmtp) REVERT: A 372 GLU cc_start: 0.7274 (tt0) cc_final: 0.6931 (tt0) REVERT: B 336 GLN cc_start: 0.8015 (tt0) cc_final: 0.7793 (tt0) REVERT: B 340 LYS cc_start: 0.7223 (tttt) cc_final: 0.6379 (tmtm) REVERT: B 372 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7345 (mt-10) REVERT: C 317 LYS cc_start: 0.7894 (mttt) cc_final: 0.7217 (mtpt) REVERT: C 338 GLU cc_start: 0.7350 (tt0) cc_final: 0.6686 (tp30) REVERT: C 340 LYS cc_start: 0.7759 (tttt) cc_final: 0.7456 (ttpp) REVERT: C 347 LYS cc_start: 0.8613 (mppt) cc_final: 0.8227 (mptp) REVERT: C 349 ARG cc_start: 0.6353 (mtm-85) cc_final: 0.4977 (mtt90) REVERT: C 353 LYS cc_start: 0.7488 (mttt) cc_final: 0.7134 (tmtp) REVERT: D 317 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7991 (mttm) REVERT: D 340 LYS cc_start: 0.7938 (tttt) cc_final: 0.7176 (tptt) REVERT: D 347 LYS cc_start: 0.7995 (mttt) cc_final: 0.7707 (mmtm) REVERT: E 317 LYS cc_start: 0.7395 (mttt) cc_final: 0.6257 (tttp) REVERT: E 338 GLU cc_start: 0.6750 (tt0) cc_final: 0.6075 (tp30) REVERT: E 340 LYS cc_start: 0.7089 (tttt) cc_final: 0.6793 (ttpp) REVERT: E 345 ASP cc_start: 0.7715 (t0) cc_final: 0.7170 (m-30) REVERT: E 351 GLN cc_start: 0.7423 (tt0) cc_final: 0.7026 (tt0) REVERT: E 353 LYS cc_start: 0.7138 (mttt) cc_final: 0.6750 (tmtp) REVERT: E 369 LYS cc_start: 0.7039 (tttt) cc_final: 0.6449 (ttmt) REVERT: F 340 LYS cc_start: 0.7209 (tttt) cc_final: 0.6367 (tptt) REVERT: F 349 ARG cc_start: 0.6143 (mtm180) cc_final: 0.4967 (mmp80) outliers start: 5 outliers final: 2 residues processed: 79 average time/residue: 3.6165 time to fit residues: 291.3375 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS 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: 0.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4523 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= 0.156 Angle : 0.434 4.234 4680 Z= 0.218 Chirality : 0.049 0.124 528 Planarity : 0.003 0.021 594 Dihedral : 4.257 11.628 462 Min Nonbonded Distance : 2.147 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: -1.63 (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 0.003 0.001 HIS B 330 PHE 0.005 0.001 PHE A 378 TYR 0.005 0.001 TYR A 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 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6328 (mt) cc_final: 0.6017 (mp) REVERT: A 317 LYS cc_start: 0.7368 (mttt) cc_final: 0.6441 (mtpt) REVERT: A 338 GLU cc_start: 0.6924 (tt0) cc_final: 0.6133 (tp30) REVERT: A 345 ASP cc_start: 0.7727 (t0) cc_final: 0.7320 (m-30) REVERT: A 351 GLN cc_start: 0.7372 (tt0) cc_final: 0.6919 (tt0) REVERT: A 353 LYS cc_start: 0.6991 (mttt) cc_final: 0.6668 (tmtp) REVERT: B 336 GLN cc_start: 0.8022 (tt0) cc_final: 0.7805 (tt0) REVERT: B 340 LYS cc_start: 0.7220 (tttt) cc_final: 0.6360 (tmtm) REVERT: C 317 LYS cc_start: 0.7824 (mttt) cc_final: 0.7141 (mtpt) REVERT: C 338 GLU cc_start: 0.7350 (tt0) cc_final: 0.6685 (tp30) REVERT: C 340 LYS cc_start: 0.7747 (tttt) cc_final: 0.7452 (ttpp) REVERT: C 347 LYS cc_start: 0.8623 (mppt) cc_final: 0.8234 (mptp) REVERT: C 349 ARG cc_start: 0.6347 (mtm-85) cc_final: 0.4989 (mtt90) REVERT: C 353 LYS cc_start: 0.7521 (mttt) cc_final: 0.7138 (tmtp) REVERT: C 358 ASP cc_start: 0.8019 (m-30) cc_final: 0.7764 (m-30) REVERT: D 317 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7969 (mttm) REVERT: D 340 LYS cc_start: 0.7940 (tttt) cc_final: 0.7180 (tptt) REVERT: D 347 LYS cc_start: 0.8003 (mttt) cc_final: 0.7689 (mmtm) REVERT: E 317 LYS cc_start: 0.7346 (mttt) cc_final: 0.6259 (tttp) REVERT: E 338 GLU cc_start: 0.6747 (tt0) cc_final: 0.6078 (tp30) REVERT: E 340 LYS cc_start: 0.7023 (tttt) cc_final: 0.6750 (ttpp) REVERT: E 345 ASP cc_start: 0.7708 (t0) cc_final: 0.7173 (m-30) REVERT: E 351 GLN cc_start: 0.7430 (tt0) cc_final: 0.7073 (tt0) REVERT: E 353 LYS cc_start: 0.7133 (mttt) cc_final: 0.6741 (tmtp) REVERT: E 369 LYS cc_start: 0.7009 (tttt) cc_final: 0.6440 (ttmp) REVERT: F 340 LYS cc_start: 0.7190 (tttt) cc_final: 0.6364 (tptt) REVERT: F 349 ARG cc_start: 0.6200 (mtm180) cc_final: 0.5003 (mmp80) outliers start: 7 outliers final: 3 residues processed: 77 average time/residue: 3.4468 time to fit residues: 271.0463 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS 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: 3.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.7579 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.239 Angle : 0.468 4.394 4680 Z= 0.237 Chirality : 0.049 0.123 528 Planarity : 0.003 0.024 594 Dihedral : 4.504 12.742 462 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % 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: -1.84 (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 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6389 (mt) cc_final: 0.6058 (mp) REVERT: A 317 LYS cc_start: 0.7386 (mttt) cc_final: 0.6447 (mtpt) REVERT: A 338 GLU cc_start: 0.6911 (tt0) cc_final: 0.6125 (tp30) REVERT: A 340 LYS cc_start: 0.7209 (tttt) cc_final: 0.6836 (ttpp) REVERT: A 345 ASP cc_start: 0.7754 (t0) cc_final: 0.7332 (m-30) REVERT: A 351 GLN cc_start: 0.7437 (tt0) cc_final: 0.6996 (tt0) REVERT: A 353 LYS cc_start: 0.6945 (mttt) cc_final: 0.6657 (tmtp) REVERT: B 336 GLN cc_start: 0.8021 (tt0) cc_final: 0.7802 (tt0) REVERT: B 340 LYS cc_start: 0.7229 (tttt) cc_final: 0.6376 (tmtm) REVERT: C 317 LYS cc_start: 0.7864 (mttt) cc_final: 0.7109 (mtpt) REVERT: C 338 GLU cc_start: 0.7368 (tt0) cc_final: 0.6692 (tp30) REVERT: C 340 LYS cc_start: 0.7766 (tttt) cc_final: 0.7442 (ttpp) REVERT: C 347 LYS cc_start: 0.8629 (mppt) cc_final: 0.8226 (mptp) REVERT: C 349 ARG cc_start: 0.6325 (mtm-85) cc_final: 0.5039 (mtt90) REVERT: C 353 LYS cc_start: 0.7539 (mttt) cc_final: 0.7177 (tmtp) REVERT: D 317 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7999 (mttm) REVERT: D 340 LYS cc_start: 0.7936 (tttt) cc_final: 0.7163 (tptt) REVERT: D 347 LYS cc_start: 0.7993 (mttt) cc_final: 0.7669 (mmtm) REVERT: D 349 ARG cc_start: 0.6551 (mtm-85) cc_final: 0.3948 (pmt-80) REVERT: E 317 LYS cc_start: 0.7358 (mttt) cc_final: 0.6253 (tttp) REVERT: E 338 GLU cc_start: 0.6796 (tt0) cc_final: 0.6131 (tp30) REVERT: E 340 LYS cc_start: 0.7033 (tttt) cc_final: 0.6716 (ttpp) REVERT: E 345 ASP cc_start: 0.7715 (t0) cc_final: 0.7168 (m-30) REVERT: E 351 GLN cc_start: 0.7477 (tt0) cc_final: 0.7079 (tt0) REVERT: E 353 LYS cc_start: 0.7131 (mttt) cc_final: 0.6736 (tmtp) REVERT: E 369 LYS cc_start: 0.7065 (tttt) cc_final: 0.6470 (ttmt) REVERT: F 340 LYS cc_start: 0.7209 (tttt) cc_final: 0.6335 (tptt) REVERT: F 349 ARG cc_start: 0.6225 (mtm180) cc_final: 0.4976 (mmp80) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 3.5393 time to fit residues: 274.5693 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 D residue 317 LYS 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: 4.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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: 0.7577 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.202 Angle : 0.451 4.379 4680 Z= 0.227 Chirality : 0.049 0.122 528 Planarity : 0.003 0.023 594 Dihedral : 4.377 12.356 462 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.77 % Allowed : 17.93 % 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: -1.85 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 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 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 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6399 (mt) cc_final: 0.6078 (mp) REVERT: A 317 LYS cc_start: 0.7390 (mttt) cc_final: 0.6480 (mtpt) REVERT: A 338 GLU cc_start: 0.6913 (tt0) cc_final: 0.6119 (tp30) REVERT: A 345 ASP cc_start: 0.7741 (t0) cc_final: 0.7351 (m-30) REVERT: A 351 GLN cc_start: 0.7437 (tt0) cc_final: 0.7005 (tt0) REVERT: A 353 LYS cc_start: 0.7019 (mttt) cc_final: 0.6673 (tmtp) REVERT: B 336 GLN cc_start: 0.8036 (tt0) cc_final: 0.7816 (tt0) REVERT: B 340 LYS cc_start: 0.7227 (tttt) cc_final: 0.6370 (tmtm) REVERT: C 338 GLU cc_start: 0.7364 (tt0) cc_final: 0.6686 (tp30) REVERT: C 340 LYS cc_start: 0.7762 (tttt) cc_final: 0.7448 (ttpp) REVERT: C 347 LYS cc_start: 0.8627 (mppt) cc_final: 0.8225 (mptp) REVERT: C 349 ARG cc_start: 0.6401 (mtm-85) cc_final: 0.5120 (mtt90) REVERT: C 353 LYS cc_start: 0.7570 (mttt) cc_final: 0.7166 (tmtp) REVERT: D 317 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7980 (mttm) REVERT: D 340 LYS cc_start: 0.7933 (tttt) cc_final: 0.7159 (tptt) REVERT: D 347 LYS cc_start: 0.7993 (mttt) cc_final: 0.7653 (mmtm) REVERT: E 317 LYS cc_start: 0.7374 (mttt) cc_final: 0.6278 (tttp) REVERT: E 338 GLU cc_start: 0.6790 (tt0) cc_final: 0.6096 (tp30) REVERT: E 340 LYS cc_start: 0.7038 (tttt) cc_final: 0.6741 (ttpp) REVERT: E 345 ASP cc_start: 0.7717 (t0) cc_final: 0.7169 (m-30) REVERT: E 351 GLN cc_start: 0.7442 (tt0) cc_final: 0.7073 (tt0) REVERT: E 353 LYS cc_start: 0.7161 (mttt) cc_final: 0.6763 (tmtp) REVERT: E 369 LYS cc_start: 0.7072 (tttt) cc_final: 0.6467 (ttmt) REVERT: F 340 LYS cc_start: 0.7188 (tttt) cc_final: 0.6343 (tptt) REVERT: F 349 ARG cc_start: 0.6381 (mtm180) cc_final: 0.4963 (mmp80) outliers start: 7 outliers final: 2 residues processed: 74 average time/residue: 3.3554 time to fit residues: 253.4423 Evaluate side-chains 72 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS 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: 4.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 2.1864 ------------------------------------------------------------------------------- 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: 0.7574 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.174 Angle : 0.442 4.273 4680 Z= 0.221 Chirality : 0.049 0.125 528 Planarity : 0.003 0.023 594 Dihedral : 4.244 12.251 462 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.85 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (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 0.004 0.001 TYR A 310 ARG 0.001 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 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6359 (mt) cc_final: 0.6040 (mp) REVERT: A 317 LYS cc_start: 0.7389 (mttt) cc_final: 0.6487 (mtpt) REVERT: A 338 GLU cc_start: 0.6932 (tt0) cc_final: 0.6143 (tp30) REVERT: A 345 ASP cc_start: 0.7722 (t0) cc_final: 0.7345 (m-30) REVERT: A 351 GLN cc_start: 0.7395 (tt0) cc_final: 0.6948 (tt0) REVERT: A 353 LYS cc_start: 0.7001 (mttt) cc_final: 0.6662 (tmtp) REVERT: B 336 GLN cc_start: 0.8028 (tt0) cc_final: 0.7817 (tt0) REVERT: B 340 LYS cc_start: 0.7222 (tttt) cc_final: 0.6370 (tmtm) REVERT: C 338 GLU cc_start: 0.7353 (tt0) cc_final: 0.6685 (tp30) REVERT: C 340 LYS cc_start: 0.7760 (tttt) cc_final: 0.7449 (ttpp) REVERT: C 347 LYS cc_start: 0.8627 (mppt) cc_final: 0.8224 (mptp) REVERT: C 349 ARG cc_start: 0.6478 (mtm-85) cc_final: 0.5194 (mtt90) REVERT: C 353 LYS cc_start: 0.7555 (mttt) cc_final: 0.7158 (tmtp) REVERT: D 317 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7968 (mttm) REVERT: D 340 LYS cc_start: 0.7925 (tttt) cc_final: 0.7171 (tptt) REVERT: D 347 LYS cc_start: 0.8023 (mttt) cc_final: 0.7687 (mmtm) REVERT: D 349 ARG cc_start: 0.6518 (mtm-85) cc_final: 0.3876 (pmt-80) REVERT: E 317 LYS cc_start: 0.7371 (mttt) cc_final: 0.6269 (tttp) REVERT: E 338 GLU cc_start: 0.6760 (tt0) cc_final: 0.6086 (tp30) REVERT: E 340 LYS cc_start: 0.7021 (tttt) cc_final: 0.6742 (ttpp) REVERT: E 345 ASP cc_start: 0.7724 (t0) cc_final: 0.7184 (m-30) REVERT: E 351 GLN cc_start: 0.7428 (tt0) cc_final: 0.7064 (tt0) REVERT: E 353 LYS cc_start: 0.7146 (mttt) cc_final: 0.6752 (tmtp) REVERT: E 369 LYS cc_start: 0.7066 (tttt) cc_final: 0.6459 (ttmt) REVERT: F 340 LYS cc_start: 0.7194 (tttt) cc_final: 0.6345 (tptt) REVERT: F 349 ARG cc_start: 0.6444 (mtm180) cc_final: 0.4998 (mmp80) outliers start: 5 outliers final: 2 residues processed: 73 average time/residue: 3.4471 time to fit residues: 256.8604 Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 317 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.137767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.129566 restraints weight = 14738.814| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.38 r_work: 0.3840 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3498 Z= 0.110 Angle : 0.419 4.088 4680 Z= 0.207 Chirality : 0.050 0.123 528 Planarity : 0.002 0.022 594 Dihedral : 3.859 11.086 462 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.51 % Allowed : 19.70 % 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: -1.65 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 330 PHE 0.002 0.000 PHE B 378 TYR 0.006 0.001 TYR A 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: 5284.69 seconds wall clock time: 92 minutes 6.09 seconds (5526.09 seconds total)