Starting phenix.real_space_refine on Wed Feb 14 07:03:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og2_20050/02_2024/6og2_20050_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og2_20050/02_2024/6og2_20050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og2_20050/02_2024/6og2_20050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og2_20050/02_2024/6og2_20050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og2_20050/02_2024/6og2_20050_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og2_20050/02_2024/6og2_20050_updated.pdb" } resolution = 4.1 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 P 6 5.49 5 S 30 5.16 5 C 5535 2.51 5 N 1608 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "F PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 355": "OE1" <-> "OE2" Residue "F ASP 367": "OD1" <-> "OD2" Residue "F TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 395": "OD1" <-> "OD2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F GLU 535": "OE1" <-> "OE2" Residue "F ASP 578": "OD1" <-> "OD2" Residue "F PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 626": "OD1" <-> "OD2" Residue "F GLU 627": "OE1" <-> "OE2" Residue "F GLU 636": "OE1" <-> "OE2" Residue "F PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 733": "OD1" <-> "OD2" Residue "F PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 815": "NH1" <-> "NH2" Residue "F GLU 826": "OE1" <-> "OE2" Residue "F GLU 850": "OE1" <-> "OE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A ASP 677": "OD1" <-> "OD2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A ASP 696": "OD1" <-> "OD2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A ASP 758": "OD1" <-> "OD2" Residue "A GLU 792": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8847 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4426 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 20, 'TRANS': 537} Chain breaks: 3 Chain: "A" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4340 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 21, 'TRANS': 526} Chain breaks: 2 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.08, per 1000 atoms: 0.57 Number of scatterers: 8847 At special positions: 0 Unit cell: (107.328, 121.776, 108.36, 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 30 16.00 P 6 15.00 O 1668 8.00 N 1608 7.00 C 5535 6.00 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 5 sheets defined 25.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'F' and resid 168 through 172 Processing helix chain 'F' and resid 184 through 194 removed outlier: 3.599A pdb=" N ILE F 191 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 223 removed outlier: 4.664A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG F 222 " --> pdb=" O GLY F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 removed outlier: 4.964A pdb=" N VAL F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.680A pdb=" N ARG F 320 " --> pdb=" O LEU F 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 316 through 320' Processing helix chain 'F' and resid 328 through 331 No H-bonds generated for 'chain 'F' and resid 328 through 331' Processing helix chain 'F' and resid 343 through 351 removed outlier: 3.865A pdb=" N LEU F 350 " --> pdb=" O THR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 374 No H-bonds generated for 'chain 'F' and resid 371 through 374' Processing helix chain 'F' and resid 386 through 392 removed outlier: 4.341A pdb=" N ILE F 391 " --> pdb=" O PRO F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 403 removed outlier: 3.849A pdb=" N SER F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 544 removed outlier: 3.778A pdb=" N ARG F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 558 No H-bonds generated for 'chain 'F' and resid 555 through 558' Processing helix chain 'F' and resid 613 through 615 No H-bonds generated for 'chain 'F' and resid 613 through 615' Processing helix chain 'F' and resid 751 through 753 No H-bonds generated for 'chain 'F' and resid 751 through 753' Processing helix chain 'F' and resid 771 through 774 No H-bonds generated for 'chain 'F' and resid 771 through 774' Processing helix chain 'F' and resid 780 through 783 No H-bonds generated for 'chain 'F' and resid 780 through 783' Processing helix chain 'F' and resid 814 through 820 Processing helix chain 'F' and resid 829 through 831 No H-bonds generated for 'chain 'F' and resid 829 through 831' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 212 through 215 No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.776A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 260 through 267' Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 343 through 351 removed outlier: 4.017A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 380 No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.682A pdb=" N ALA A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 533 through 544 Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.836A pdb=" N ILE A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 3.668A pdb=" N ALA A 617 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 692 through 695 No H-bonds generated for 'chain 'A' and resid 692 through 695' Processing helix chain 'A' and resid 736 through 739 No H-bonds generated for 'chain 'A' and resid 736 through 739' Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 751 through 756 removed outlier: 4.062A pdb=" N ASN A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 751 through 756' Processing helix chain 'A' and resid 769 through 774 removed outlier: 3.780A pdb=" N SER A 773 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 800 through 803 No H-bonds generated for 'chain 'A' and resid 800 through 803' Processing helix chain 'A' and resid 817 through 820 Processing sheet with id= A, first strand: chain 'F' and resid 334 through 338 removed outlier: 7.285A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLY F 206 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR F 314 " --> pdb=" O GLY F 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 310 through 313 removed outlier: 3.564A pdb=" N GLN A 334 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 203 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 601 through 604 removed outlier: 7.012A pdb=" N GLU A 759 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU A 604 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 761 " --> pdb=" O LEU A 604 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 674 through 676 Processing sheet with id= E, first strand: chain 'A' and resid 698 through 700 77 hydrogen bonds defined for protein. 222 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: 1.91 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3029 1.34 - 1.46: 1555 1.46 - 1.58: 4330 1.58 - 1.70: 9 1.70 - 1.82: 56 Bond restraints: 8979 Sorted by residual: bond pdb=" CB ILE F 825 " pdb=" CG2 ILE F 825 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.82e+00 bond pdb=" CB GLU F 254 " pdb=" CG GLU F 254 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.75e+00 bond pdb=" C GLU F 207 " pdb=" N PRO F 208 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.41e+00 bond pdb=" CB ASN A 200 " pdb=" CG ASN A 200 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.37e+00 bond pdb=" CB THR A 700 " pdb=" CG2 THR A 700 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 ... (remaining 8974 not shown) Histogram of bond angle deviations from ideal: 98.81 - 106.24: 235 106.24 - 113.68: 4911 113.68 - 121.12: 4347 121.12 - 128.55: 2581 128.55 - 135.99: 49 Bond angle restraints: 12123 Sorted by residual: angle pdb=" N ILE A 793 " pdb=" CA ILE A 793 " pdb=" C ILE A 793 " ideal model delta sigma weight residual 111.88 104.51 7.37 1.06e+00 8.90e-01 4.83e+01 angle pdb=" N PHE A 601 " pdb=" CA PHE A 601 " pdb=" C PHE A 601 " ideal model delta sigma weight residual 108.34 114.40 -6.06 1.31e+00 5.83e-01 2.14e+01 angle pdb=" N VAL F 745 " pdb=" CA VAL F 745 " pdb=" C VAL F 745 " ideal model delta sigma weight residual 112.12 108.45 3.67 8.40e-01 1.42e+00 1.91e+01 angle pdb=" N GLY F 730 " pdb=" CA GLY F 730 " pdb=" C GLY F 730 " ideal model delta sigma weight residual 113.18 123.08 -9.90 2.37e+00 1.78e-01 1.74e+01 angle pdb=" N THR F 712 " pdb=" CA THR F 712 " pdb=" C THR F 712 " ideal model delta sigma weight residual 109.94 103.45 6.49 1.57e+00 4.06e-01 1.71e+01 ... (remaining 12118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 5217 29.58 - 59.16: 279 59.16 - 88.75: 28 88.75 - 118.33: 1 118.33 - 147.91: 2 Dihedral angle restraints: 5527 sinusoidal: 2344 harmonic: 3183 Sorted by residual: dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 87.91 -147.91 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 72.36 -132.37 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" CA TYR F 783 " pdb=" C TYR F 783 " pdb=" N LYS F 784 " pdb=" CA LYS F 784 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1024 0.063 - 0.127: 282 0.127 - 0.190: 54 0.190 - 0.253: 9 0.253 - 0.316: 3 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CB ILE F 166 " pdb=" CA ILE F 166 " pdb=" CG1 ILE F 166 " pdb=" CG2 ILE F 166 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB VAL A 577 " pdb=" CA VAL A 577 " pdb=" CG1 VAL A 577 " pdb=" CG2 VAL A 577 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASN F 827 " pdb=" N ASN F 827 " pdb=" C ASN F 827 " pdb=" CB ASN F 827 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1369 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 340 " 0.051 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO A 341 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 683 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO F 684 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 684 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 684 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 300 " 0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO A 301 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " 0.040 5.00e-02 4.00e+02 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 967 2.75 - 3.29: 8105 3.29 - 3.82: 14514 3.82 - 4.36: 17233 4.36 - 4.90: 27751 Nonbonded interactions: 68570 Sorted by model distance: nonbonded pdb=" O LEU F 724 " pdb=" CG1 ILE F 725 " model vdw 2.211 3.440 nonbonded pdb=" OD1 ASP A 167 " pdb=" OG1 THR A 169 " model vdw 2.259 2.440 nonbonded pdb=" CD2 LEU F 802 " pdb=" CD1 LEU F 803 " model vdw 2.266 3.880 nonbonded pdb=" O PRO F 765 " pdb=" O LEU F 766 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLN F 726 " pdb=" OH TYR F 808 " model vdw 2.287 2.440 ... (remaining 68565 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' and (resid 161 through 648 or resid 661 through 835 or resid 902)) selection = (chain 'F' and (resid 161 through 835 or resid 901)) } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.140 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: 0.010 Extract box with map and model: 3.590 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.880 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5043 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 : 0.006 0.055 8979 Z= 0.365 Angle : 1.113 9.900 12123 Z= 0.599 Chirality : 0.061 0.316 1372 Planarity : 0.007 0.077 1581 Dihedral : 17.539 147.910 3471 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.27 % Favored : 87.55 % Rotamer: Outliers : 0.43 % Allowed : 14.39 % Favored : 85.18 % 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: -5.21 (0.19), residues: 1092 helix: -4.86 (0.13), residues: 292 sheet: -2.55 (0.50), residues: 78 loop : -3.13 (0.19), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 543 HIS 0.007 0.002 HIS F 770 PHE 0.020 0.003 PHE F 763 TYR 0.022 0.003 TYR A 653 ARG 0.009 0.001 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 267 time to evaluate : 0.945 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: F 191 ILE cc_start: 0.8494 (pt) cc_final: 0.7791 (pt) REVERT: F 205 ILE cc_start: 0.7985 (mt) cc_final: 0.7782 (mt) REVERT: F 238 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7302 (mp) REVERT: F 278 ASP cc_start: 0.7920 (t0) cc_final: 0.7630 (t0) REVERT: F 279 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7532 (pt0) REVERT: F 401 ILE cc_start: 0.8335 (mt) cc_final: 0.8001 (tp) REVERT: F 712 THR cc_start: 0.6400 (m) cc_final: 0.6144 (p) REVERT: A 185 GLU cc_start: 0.7145 (pm20) cc_final: 0.5974 (mp0) REVERT: A 204 LEU cc_start: 0.7168 (mp) cc_final: 0.6766 (mt) REVERT: A 299 LEU cc_start: 0.7753 (mm) cc_final: 0.7515 (tp) REVERT: A 314 THR cc_start: 0.6811 (t) cc_final: 0.6589 (t) REVERT: A 543 TRP cc_start: 0.7556 (m-10) cc_final: 0.7354 (m-10) REVERT: A 564 GLN cc_start: 0.7585 (mp10) cc_final: 0.7131 (tt0) REVERT: A 656 TYR cc_start: 0.7192 (t80) cc_final: 0.6949 (t80) REVERT: A 713 VAL cc_start: 0.6134 (t) cc_final: 0.5811 (t) outliers start: 4 outliers final: 1 residues processed: 271 average time/residue: 0.2884 time to fit residues: 98.4634 Evaluate side-chains 157 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 ASN ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 857 GLN A 174 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN A 692 GLN A 736 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8979 Z= 0.208 Angle : 0.743 8.110 12123 Z= 0.370 Chirality : 0.047 0.173 1372 Planarity : 0.005 0.058 1581 Dihedral : 9.033 141.387 1256 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 0.21 % Allowed : 5.97 % Favored : 93.82 % 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: -4.56 (0.22), residues: 1092 helix: -4.02 (0.18), residues: 339 sheet: -1.77 (0.60), residues: 71 loop : -2.75 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 543 HIS 0.007 0.001 HIS A 360 PHE 0.018 0.002 PHE A 623 TYR 0.011 0.001 TYR F 319 ARG 0.014 0.001 ARG F 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7214 (mtp180) REVERT: F 199 LYS cc_start: 0.8015 (ptmt) cc_final: 0.7725 (ptmt) REVERT: F 205 ILE cc_start: 0.8383 (mt) cc_final: 0.8103 (mt) REVERT: F 399 SER cc_start: 0.7567 (t) cc_final: 0.7266 (p) REVERT: F 401 ILE cc_start: 0.8311 (mt) cc_final: 0.7944 (tp) REVERT: F 712 THR cc_start: 0.5821 (m) cc_final: 0.5532 (p) REVERT: A 179 PRO cc_start: 0.6159 (Cg_exo) cc_final: 0.4634 (Cg_endo) REVERT: A 310 CYS cc_start: 0.6497 (t) cc_final: 0.5877 (p) REVERT: A 314 THR cc_start: 0.7758 (t) cc_final: 0.6647 (t) REVERT: A 535 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8251 (mm-30) REVERT: A 634 MET cc_start: 0.7210 (mmm) cc_final: 0.6736 (mmp) REVERT: A 646 LEU cc_start: 0.7588 (pt) cc_final: 0.7120 (mt) REVERT: A 664 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6799 (tm-30) REVERT: A 709 PHE cc_start: 0.8118 (m-80) cc_final: 0.7876 (m-80) REVERT: A 712 THR cc_start: 0.5824 (p) cc_final: 0.5579 (p) outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.2629 time to fit residues: 65.3620 Evaluate side-chains 146 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 0.0050 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 776 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 711 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8979 Z= 0.178 Angle : 0.685 7.786 12123 Z= 0.338 Chirality : 0.045 0.167 1372 Planarity : 0.005 0.045 1581 Dihedral : 8.233 135.575 1256 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.23), residues: 1092 helix: -3.42 (0.21), residues: 341 sheet: -1.21 (0.60), residues: 79 loop : -2.42 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 543 HIS 0.006 0.001 HIS A 747 PHE 0.011 0.001 PHE A 709 TYR 0.015 0.001 TYR F 319 ARG 0.009 0.001 ARG A 667 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7267 (mtp180) REVERT: F 205 ILE cc_start: 0.8502 (mt) cc_final: 0.8285 (mt) REVERT: F 217 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8418 (mt-10) REVERT: F 319 TYR cc_start: 0.7271 (t80) cc_final: 0.6755 (t80) REVERT: F 401 ILE cc_start: 0.8334 (mt) cc_final: 0.7925 (tp) REVERT: F 622 MET cc_start: 0.3807 (tpt) cc_final: 0.3106 (mmm) REVERT: A 177 LEU cc_start: 0.8474 (mt) cc_final: 0.8082 (mt) REVERT: A 179 PRO cc_start: 0.6072 (Cg_exo) cc_final: 0.5721 (Cg_endo) REVERT: A 185 GLU cc_start: 0.8164 (tp30) cc_final: 0.7912 (tp30) REVERT: A 314 THR cc_start: 0.7761 (t) cc_final: 0.7248 (t) REVERT: A 353 LEU cc_start: 0.8427 (tp) cc_final: 0.7949 (tp) REVERT: A 535 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 595 ASN cc_start: 0.7435 (t0) cc_final: 0.6979 (t0) REVERT: A 646 LEU cc_start: 0.7398 (pt) cc_final: 0.7151 (mt) REVERT: A 709 PHE cc_start: 0.7728 (m-80) cc_final: 0.7518 (m-80) REVERT: A 712 THR cc_start: 0.6167 (p) cc_final: 0.5957 (p) REVERT: A 713 VAL cc_start: 0.7321 (t) cc_final: 0.5773 (t) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2538 time to fit residues: 57.2467 Evaluate side-chains 133 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 0.0170 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 857 GLN A 281 HIS A 309 HIS A 641 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8979 Z= 0.168 Angle : 0.657 7.250 12123 Z= 0.321 Chirality : 0.045 0.173 1372 Planarity : 0.004 0.040 1581 Dihedral : 7.803 133.051 1256 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.24), residues: 1092 helix: -3.14 (0.22), residues: 351 sheet: -1.27 (0.59), residues: 84 loop : -2.09 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 543 HIS 0.006 0.001 HIS F 770 PHE 0.010 0.001 PHE F 763 TYR 0.009 0.001 TYR F 319 ARG 0.004 0.000 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 167 ASP cc_start: 0.6541 (t0) cc_final: 0.5320 (m-30) REVERT: F 188 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7322 (mtp180) REVERT: F 199 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7981 (ptmt) REVERT: F 217 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8520 (mt-10) REVERT: F 552 MET cc_start: 0.5540 (mpp) cc_final: 0.5195 (mmp) REVERT: A 177 LEU cc_start: 0.8459 (mt) cc_final: 0.7995 (mt) REVERT: A 314 THR cc_start: 0.7477 (t) cc_final: 0.6990 (t) REVERT: A 595 ASN cc_start: 0.7676 (t0) cc_final: 0.7191 (t0) REVERT: A 646 LEU cc_start: 0.7458 (pt) cc_final: 0.7180 (mt) REVERT: A 713 VAL cc_start: 0.7276 (t) cc_final: 0.5848 (t) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2319 time to fit residues: 52.0722 Evaluate side-chains 120 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 89 optimal weight: 0.0470 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8979 Z= 0.228 Angle : 0.705 7.229 12123 Z= 0.351 Chirality : 0.047 0.165 1372 Planarity : 0.004 0.038 1581 Dihedral : 7.896 142.771 1256 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.24), residues: 1092 helix: -3.16 (0.21), residues: 375 sheet: -1.56 (0.58), residues: 85 loop : -1.95 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.005 0.001 HIS F 281 PHE 0.012 0.002 PHE A 276 TYR 0.012 0.001 TYR A 653 ARG 0.006 0.001 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7405 (mtp180) REVERT: F 196 ARG cc_start: 0.7576 (ptp-170) cc_final: 0.7091 (ptp-170) REVERT: F 217 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8481 (tt0) REVERT: F 279 GLU cc_start: 0.7730 (pt0) cc_final: 0.7499 (pt0) REVERT: F 401 ILE cc_start: 0.8320 (mt) cc_final: 0.8097 (mt) REVERT: F 629 MET cc_start: 0.6539 (pmm) cc_final: 0.6311 (pmm) REVERT: A 353 LEU cc_start: 0.8179 (tp) cc_final: 0.7919 (tp) REVERT: A 653 TYR cc_start: 0.5761 (t80) cc_final: 0.5102 (m-80) REVERT: A 713 VAL cc_start: 0.7450 (t) cc_final: 0.6916 (t) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2044 time to fit residues: 46.5826 Evaluate side-chains 132 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 0.3980 chunk 48 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 0.0030 chunk 101 optimal weight: 0.6980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 857 GLN A 272 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 641 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8979 Z= 0.167 Angle : 0.670 7.309 12123 Z= 0.327 Chirality : 0.045 0.169 1372 Planarity : 0.004 0.036 1581 Dihedral : 7.454 139.693 1256 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 0.11 % Allowed : 2.24 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.24), residues: 1092 helix: -2.81 (0.24), residues: 358 sheet: -1.31 (0.59), residues: 73 loop : -1.93 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 543 HIS 0.006 0.001 HIS A 641 PHE 0.011 0.001 PHE F 763 TYR 0.012 0.001 TYR F 319 ARG 0.004 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 0.989 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: F 188 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7363 (mtp180) REVERT: F 217 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8492 (mt-10) REVERT: F 279 GLU cc_start: 0.7563 (pt0) cc_final: 0.7359 (pt0) REVERT: F 399 SER cc_start: 0.8416 (t) cc_final: 0.8102 (p) REVERT: F 401 ILE cc_start: 0.8513 (mt) cc_final: 0.8099 (mm) REVERT: F 629 MET cc_start: 0.6744 (pmm) cc_final: 0.6527 (pmm) REVERT: A 351 ARG cc_start: 0.8587 (ttm110) cc_final: 0.8290 (tpp80) REVERT: A 403 MET cc_start: 0.8110 (tpp) cc_final: 0.7728 (tpt) REVERT: A 646 LEU cc_start: 0.7736 (pt) cc_final: 0.7106 (mt) REVERT: A 653 TYR cc_start: 0.5787 (t80) cc_final: 0.5124 (m-80) REVERT: A 664 GLU cc_start: 0.6646 (tm-30) cc_final: 0.6421 (tm-30) REVERT: A 713 VAL cc_start: 0.7295 (t) cc_final: 0.6847 (t) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.2186 time to fit residues: 50.4518 Evaluate side-chains 132 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.0170 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.0000 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.0270 chunk 41 optimal weight: 4.9990 overall best weight: 0.2480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 281 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 711 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.7375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8979 Z= 0.151 Angle : 0.654 7.317 12123 Z= 0.317 Chirality : 0.045 0.180 1372 Planarity : 0.004 0.035 1581 Dihedral : 7.172 141.224 1256 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 0.21 % Allowed : 2.13 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.24), residues: 1092 helix: -2.59 (0.25), residues: 357 sheet: -1.56 (0.56), residues: 85 loop : -1.84 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 543 HIS 0.005 0.001 HIS A 747 PHE 0.011 0.001 PHE F 763 TYR 0.019 0.001 TYR F 319 ARG 0.007 0.000 ARG F 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7421 (mtp180) REVERT: F 399 SER cc_start: 0.8463 (t) cc_final: 0.8123 (p) REVERT: F 401 ILE cc_start: 0.8464 (mt) cc_final: 0.8024 (mm) REVERT: F 552 MET cc_start: 0.4846 (mmt) cc_final: 0.3877 (mmp) REVERT: F 770 HIS cc_start: 0.7713 (t70) cc_final: 0.7404 (t-90) REVERT: A 273 VAL cc_start: 0.9418 (m) cc_final: 0.9030 (t) REVERT: A 351 ARG cc_start: 0.8596 (ttm110) cc_final: 0.8318 (tpp80) REVERT: A 403 MET cc_start: 0.8124 (tpp) cc_final: 0.7770 (tpt) REVERT: A 550 ARG cc_start: 0.7539 (ptm160) cc_final: 0.7289 (ttp-110) REVERT: A 595 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7300 (t0) REVERT: A 664 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6427 (tm-30) REVERT: A 713 VAL cc_start: 0.7352 (t) cc_final: 0.6657 (t) outliers start: 2 outliers final: 1 residues processed: 155 average time/residue: 0.1929 time to fit residues: 42.5287 Evaluate side-chains 129 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 82 optimal weight: 0.3980 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 778 GLN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.7782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8979 Z= 0.175 Angle : 0.674 10.201 12123 Z= 0.326 Chirality : 0.046 0.168 1372 Planarity : 0.004 0.035 1581 Dihedral : 7.235 146.126 1256 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.25), residues: 1092 helix: -2.62 (0.24), residues: 359 sheet: -1.72 (0.62), residues: 68 loop : -1.59 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 543 HIS 0.004 0.001 HIS A 747 PHE 0.010 0.001 PHE F 763 TYR 0.010 0.001 TYR A 319 ARG 0.006 0.000 ARG F 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7474 (mtp180) REVERT: F 217 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8349 (mt-10) REVERT: F 335 LYS cc_start: 0.8953 (mppt) cc_final: 0.8718 (mmtp) REVERT: F 399 SER cc_start: 0.8590 (t) cc_final: 0.8320 (p) REVERT: F 401 ILE cc_start: 0.8494 (mt) cc_final: 0.8039 (mm) REVERT: F 552 MET cc_start: 0.4869 (mmt) cc_final: 0.3873 (mmp) REVERT: F 629 MET cc_start: 0.6868 (pmm) cc_final: 0.6435 (pmm) REVERT: F 770 HIS cc_start: 0.7834 (t70) cc_final: 0.7504 (t-90) REVERT: A 403 MET cc_start: 0.8085 (tpp) cc_final: 0.7766 (tpt) REVERT: A 533 ASP cc_start: 0.7484 (p0) cc_final: 0.7212 (p0) REVERT: A 578 ASP cc_start: 0.8213 (m-30) cc_final: 0.7799 (m-30) REVERT: A 650 PRO cc_start: 0.7975 (Cg_endo) cc_final: 0.7445 (Cg_exo) REVERT: A 653 TYR cc_start: 0.6022 (t80) cc_final: 0.4759 (m-80) REVERT: A 699 LEU cc_start: 0.8807 (tt) cc_final: 0.8577 (tt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1883 time to fit residues: 40.1738 Evaluate side-chains 125 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 0.0070 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 309 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS A 711 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.8250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8979 Z= 0.201 Angle : 0.684 7.836 12123 Z= 0.338 Chirality : 0.047 0.183 1372 Planarity : 0.004 0.059 1581 Dihedral : 7.439 150.269 1256 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.11 % Allowed : 0.96 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.25), residues: 1092 helix: -2.54 (0.25), residues: 346 sheet: -2.04 (0.60), residues: 70 loop : -1.56 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 543 HIS 0.009 0.001 HIS F 281 PHE 0.012 0.002 PHE A 709 TYR 0.010 0.001 TYR F 783 ARG 0.006 0.000 ARG F 556 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7467 (mtp180) REVERT: F 195 GLN cc_start: 0.8129 (mt0) cc_final: 0.7777 (mt0) REVERT: F 199 LYS cc_start: 0.8354 (ptmt) cc_final: 0.8126 (ptmt) REVERT: F 217 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8265 (mt-10) REVERT: F 279 GLU cc_start: 0.7440 (tt0) cc_final: 0.7145 (tp30) REVERT: F 281 HIS cc_start: 0.6983 (p-80) cc_final: 0.6591 (p-80) REVERT: F 319 TYR cc_start: 0.7086 (t80) cc_final: 0.6263 (t80) REVERT: F 401 ILE cc_start: 0.8530 (mt) cc_final: 0.8152 (mm) REVERT: F 552 MET cc_start: 0.4945 (mmt) cc_final: 0.4037 (mmp) REVERT: F 629 MET cc_start: 0.6797 (pmm) cc_final: 0.6350 (pmm) REVERT: F 770 HIS cc_start: 0.7942 (t70) cc_final: 0.7492 (t70) REVERT: A 403 MET cc_start: 0.8121 (tpp) cc_final: 0.7665 (tpt) REVERT: A 535 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 578 ASP cc_start: 0.8394 (m-30) cc_final: 0.8019 (m-30) REVERT: A 653 TYR cc_start: 0.6107 (t80) cc_final: 0.5529 (t80) REVERT: A 716 MET cc_start: 0.8845 (mtp) cc_final: 0.8598 (mtm) outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 0.1852 time to fit residues: 38.6904 Evaluate side-chains 123 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 0.0570 chunk 99 optimal weight: 8.9990 chunk 86 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.8682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8979 Z= 0.202 Angle : 0.694 8.336 12123 Z= 0.342 Chirality : 0.047 0.161 1372 Planarity : 0.004 0.075 1581 Dihedral : 7.532 147.245 1256 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -2.92 (0.25), residues: 1092 helix: -2.63 (0.24), residues: 355 sheet: -2.16 (0.61), residues: 72 loop : -1.51 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 543 HIS 0.005 0.001 HIS A 568 PHE 0.012 0.002 PHE A 603 TYR 0.009 0.001 TYR F 783 ARG 0.009 0.001 ARG F 556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7489 (mtp180) REVERT: F 195 GLN cc_start: 0.8245 (mt0) cc_final: 0.7887 (mt0) REVERT: F 199 LYS cc_start: 0.8356 (ptmt) cc_final: 0.8050 (ptmt) REVERT: F 217 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8313 (mt-10) REVERT: F 279 GLU cc_start: 0.7526 (tt0) cc_final: 0.7312 (tt0) REVERT: F 319 TYR cc_start: 0.6989 (t80) cc_final: 0.6275 (t80) REVERT: F 401 ILE cc_start: 0.8663 (mt) cc_final: 0.8462 (mt) REVERT: F 552 MET cc_start: 0.4950 (mmt) cc_final: 0.3972 (mmp) REVERT: F 598 ILE cc_start: 0.8027 (mm) cc_final: 0.7738 (mp) REVERT: F 629 MET cc_start: 0.6505 (pmm) cc_final: 0.6010 (pmm) REVERT: F 695 ASP cc_start: 0.3429 (p0) cc_final: 0.3167 (p0) REVERT: F 770 HIS cc_start: 0.8056 (t70) cc_final: 0.7597 (t-90) REVERT: A 177 LEU cc_start: 0.8764 (mm) cc_final: 0.8493 (mt) REVERT: A 201 ASN cc_start: 0.7690 (m-40) cc_final: 0.7323 (m-40) REVERT: A 310 CYS cc_start: 0.8197 (p) cc_final: 0.7734 (p) REVERT: A 403 MET cc_start: 0.8148 (tpp) cc_final: 0.7639 (tpt) REVERT: A 578 ASP cc_start: 0.8458 (m-30) cc_final: 0.8110 (m-30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1922 time to fit residues: 40.1171 Evaluate side-chains 127 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.0010 chunk 86 optimal weight: 0.0870 chunk 36 optimal weight: 0.0050 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.0010 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 221 GLN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.201212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.172513 restraints weight = 23713.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.174326 restraints weight = 16614.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.174411 restraints weight = 11987.347| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.8738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8979 Z= 0.146 Angle : 0.664 7.951 12123 Z= 0.319 Chirality : 0.045 0.164 1372 Planarity : 0.004 0.069 1581 Dihedral : 6.993 137.994 1256 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -2.68 (0.25), residues: 1092 helix: -2.38 (0.26), residues: 341 sheet: -1.94 (0.62), residues: 69 loop : -1.43 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 543 HIS 0.005 0.001 HIS A 281 PHE 0.013 0.001 PHE A 601 TYR 0.005 0.001 TYR F 808 ARG 0.005 0.000 ARG F 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.83 seconds wall clock time: 38 minutes 27.72 seconds (2307.72 seconds total)