Starting phenix.real_space_refine on Sun Oct 13 12:23:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr2_17832/10_2024/8pr2_17832.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr2_17832/10_2024/8pr2_17832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr2_17832/10_2024/8pr2_17832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr2_17832/10_2024/8pr2_17832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr2_17832/10_2024/8pr2_17832.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr2_17832/10_2024/8pr2_17832.cif" } resolution = 3.8 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= 0.001 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 9396 2.51 5 N 2679 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 14906 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 917 Classifications: {'peptide': 106} Link IDs: {'TRANS': 105} Chain: "C" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 917 Classifications: {'peptide': 106} Link IDs: {'TRANS': 105} Chain: "f" Number of atoms: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5865 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 19, 'TRANS': 691} Chain breaks: 2 Chain: "h" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 17, 'TRANS': 353} Chain: "j" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 202 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "m" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4108 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 15, 'TRANS': 481} Chain breaks: 3 Time building chain proxies: 8.84, per 1000 atoms: 0.59 Number of scatterers: 14906 At special positions: 0 Unit cell: (112.254, 127.08, 201.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2780 8.00 N 2679 7.00 C 9396 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 2.5 seconds 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3502 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 68.3% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'B' and resid 65 through 170 removed outlier: 3.683A pdb=" N VAL B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 170 Processing helix chain 'f' and resid 247 through 261 removed outlier: 4.026A pdb=" N VAL f 259 " --> pdb=" O GLU f 255 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS f 261 " --> pdb=" O GLN f 257 " (cutoff:3.500A) Processing helix chain 'f' and resid 270 through 293 removed outlier: 3.565A pdb=" N GLU f 274 " --> pdb=" O THR f 270 " (cutoff:3.500A) Processing helix chain 'f' and resid 294 through 307 removed outlier: 3.602A pdb=" N LEU f 298 " --> pdb=" O SER f 294 " (cutoff:3.500A) Processing helix chain 'f' and resid 309 through 319 removed outlier: 4.061A pdb=" N THR f 313 " --> pdb=" O ARG f 309 " (cutoff:3.500A) Processing helix chain 'f' and resid 321 through 332 Processing helix chain 'f' and resid 332 through 337 Processing helix chain 'f' and resid 340 through 346 removed outlier: 3.501A pdb=" N LEU f 344 " --> pdb=" O PRO f 340 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER f 346 " --> pdb=" O ASN f 342 " (cutoff:3.500A) Processing helix chain 'f' and resid 349 through 364 Processing helix chain 'f' and resid 365 through 368 removed outlier: 3.959A pdb=" N ARG f 368 " --> pdb=" O ARG f 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 365 through 368' Processing helix chain 'f' and resid 373 through 400 Processing helix chain 'f' and resid 405 through 439 removed outlier: 3.571A pdb=" N PHE f 409 " --> pdb=" O ALA f 405 " (cutoff:3.500A) Processing helix chain 'f' and resid 455 through 483 removed outlier: 4.602A pdb=" N LEU f 459 " --> pdb=" O ALA f 455 " (cutoff:3.500A) Processing helix chain 'f' and resid 513 through 533 removed outlier: 4.022A pdb=" N ALA f 517 " --> pdb=" O ASP f 513 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL f 533 " --> pdb=" O ASN f 529 " (cutoff:3.500A) Processing helix chain 'f' and resid 539 through 574 removed outlier: 4.424A pdb=" N ARG f 559 " --> pdb=" O GLU f 555 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL f 560 " --> pdb=" O ARG f 556 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR f 574 " --> pdb=" O ASP f 570 " (cutoff:3.500A) Processing helix chain 'f' and resid 577 through 586 Processing helix chain 'f' and resid 588 through 592 removed outlier: 3.602A pdb=" N LEU f 591 " --> pdb=" O PHE f 588 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE f 592 " --> pdb=" O ASN f 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 588 through 592' Processing helix chain 'f' and resid 596 through 604 removed outlier: 3.816A pdb=" N ALA f 600 " --> pdb=" O HIS f 596 " (cutoff:3.500A) Processing helix chain 'f' and resid 604 through 625 removed outlier: 3.624A pdb=" N VAL f 625 " --> pdb=" O ASP f 621 " (cutoff:3.500A) Processing helix chain 'f' and resid 630 through 639 removed outlier: 3.997A pdb=" N LYS f 634 " --> pdb=" O SER f 630 " (cutoff:3.500A) Processing helix chain 'f' and resid 642 through 670 Processing helix chain 'f' and resid 676 through 693 Processing helix chain 'f' and resid 695 through 710 removed outlier: 3.529A pdb=" N PHE f 699 " --> pdb=" O THR f 695 " (cutoff:3.500A) Processing helix chain 'f' and resid 740 through 754 removed outlier: 3.848A pdb=" N ILE f 744 " --> pdb=" O LEU f 740 " (cutoff:3.500A) Processing helix chain 'f' and resid 761 through 798 Proline residue: f 776 - end of helix removed outlier: 3.658A pdb=" N SER f 780 " --> pdb=" O PRO f 776 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG f 798 " --> pdb=" O LYS f 794 " (cutoff:3.500A) Processing helix chain 'f' and resid 799 through 802 removed outlier: 3.554A pdb=" N SER f 802 " --> pdb=" O ASN f 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 799 through 802' Processing helix chain 'f' and resid 805 through 820 Processing helix chain 'f' and resid 828 through 863 removed outlier: 3.543A pdb=" N TYR f 832 " --> pdb=" O LYS f 828 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL f 833 " --> pdb=" O LEU f 829 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN f 834 " --> pdb=" O ASP f 830 " (cutoff:3.500A) Processing helix chain 'f' and resid 870 through 891 removed outlier: 3.641A pdb=" N PHE f 874 " --> pdb=" O ASP f 870 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS f 891 " --> pdb=" O ASP f 887 " (cutoff:3.500A) Processing helix chain 'f' and resid 895 through 923 removed outlier: 3.555A pdb=" N TRP f 899 " --> pdb=" O ASN f 895 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU f 906 " --> pdb=" O LYS f 902 " (cutoff:3.500A) Processing helix chain 'f' and resid 986 through 995 removed outlier: 4.110A pdb=" N VAL f 992 " --> pdb=" O ALA f 988 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL f 993 " --> pdb=" O TRP f 989 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER f 995 " --> pdb=" O MET f 991 " (cutoff:3.500A) Processing helix chain 'f' and resid 1013 through 1018 Processing helix chain 'f' and resid 1030 through 1039 removed outlier: 3.930A pdb=" N ALA f1039 " --> pdb=" O GLU f1035 " (cutoff:3.500A) Processing helix chain 'h' and resid 574 through 579 Processing helix chain 'h' and resid 583 through 608 Processing helix chain 'j' and resid 358 through 373 Processing helix chain 'm' and resid 178 through 198 Processing helix chain 'm' and resid 242 through 261 Processing helix chain 'm' and resid 270 through 293 Processing helix chain 'm' and resid 294 through 307 Processing helix chain 'm' and resid 309 through 318 removed outlier: 3.699A pdb=" N THR m 313 " --> pdb=" O ARG m 309 " (cutoff:3.500A) Processing helix chain 'm' and resid 321 through 337 removed outlier: 3.669A pdb=" N ALA m 325 " --> pdb=" O GLY m 321 " (cutoff:3.500A) Proline residue: m 334 - end of helix Processing helix chain 'm' and resid 340 through 347 removed outlier: 3.791A pdb=" N LEU m 344 " --> pdb=" O PRO m 340 " (cutoff:3.500A) Processing helix chain 'm' and resid 349 through 364 Processing helix chain 'm' and resid 365 through 369 removed outlier: 4.084A pdb=" N ARG m 368 " --> pdb=" O ARG m 365 " (cutoff:3.500A) Processing helix chain 'm' and resid 373 through 400 Processing helix chain 'm' and resid 401 through 404 removed outlier: 3.579A pdb=" N VAL m 404 " --> pdb=" O LEU m 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 401 through 404' Processing helix chain 'm' and resid 405 through 440 Processing helix chain 'm' and resid 456 through 484 removed outlier: 3.719A pdb=" N GLN m 472 " --> pdb=" O LYS m 468 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL m 479 " --> pdb=" O GLN m 475 " (cutoff:3.500A) Processing helix chain 'm' and resid 514 through 532 Processing helix chain 'm' and resid 539 through 569 Processing helix chain 'm' and resid 570 through 572 No H-bonds generated for 'chain 'm' and resid 570 through 572' Processing helix chain 'm' and resid 577 through 588 Processing helix chain 'm' and resid 589 through 593 removed outlier: 3.896A pdb=" N VAL m 593 " --> pdb=" O ALA m 590 " (cutoff:3.500A) Processing helix chain 'm' and resid 594 through 601 removed outlier: 3.531A pdb=" N ILE m 601 " --> pdb=" O ILE m 597 " (cutoff:3.500A) Processing helix chain 'm' and resid 602 through 623 removed outlier: 3.836A pdb=" N THR m 606 " --> pdb=" O ARG m 602 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN m 607 " --> pdb=" O GLU m 603 " (cutoff:3.500A) Processing helix chain 'm' and resid 630 through 639 removed outlier: 4.115A pdb=" N LYS m 634 " --> pdb=" O SER m 630 " (cutoff:3.500A) Processing helix chain 'm' and resid 642 through 670 Processing helix chain 'm' and resid 672 through 676 removed outlier: 3.553A pdb=" N ASN m 675 " --> pdb=" O GLY m 672 " (cutoff:3.500A) Processing helix chain 'm' and resid 678 through 692 removed outlier: 3.613A pdb=" N LEU m 682 " --> pdb=" O GLU m 678 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS m 692 " --> pdb=" O SER m 688 " (cutoff:3.500A) Processing helix chain 'm' and resid 695 through 707 removed outlier: 3.528A pdb=" N PHE m 699 " --> pdb=" O THR m 695 " (cutoff:3.500A) Processing helix chain 'm' and resid 746 through 754 Processing helix chain 'm' and resid 761 through 766 removed outlier: 3.509A pdb=" N VAL m 765 " --> pdb=" O PRO m 761 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN m 766 " --> pdb=" O LEU m 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 761 through 766' Processing sheet with id=AA1, first strand: chain 'f' and resid 718 through 723 Processing sheet with id=AA2, first strand: chain 'h' and resid 239 through 245 removed outlier: 5.835A pdb=" N LEU h 241 " --> pdb=" O ASP h 572 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASP h 572 " --> pdb=" O LEU h 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG h 243 " --> pdb=" O ILE h 570 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 256 through 261 removed outlier: 4.327A pdb=" N CYS h 258 " --> pdb=" O SER h 272 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL h 286 " --> pdb=" O TYR h 273 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY h 285 " --> pdb=" O CYS h 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 309 through 314 Processing sheet with id=AA5, first strand: chain 'h' and resid 358 through 365 removed outlier: 3.878A pdb=" N CYS h 360 " --> pdb=" O ILE h 375 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS h 380 " --> pdb=" O SER h 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'h' and resid 408 through 412 Processing sheet with id=AA7, first strand: chain 'h' and resid 453 through 458 removed outlier: 3.647A pdb=" N SER h 475 " --> pdb=" O THR h 479 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR h 479 " --> pdb=" O SER h 475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 501 through 506 removed outlier: 4.062A pdb=" N ASP h 503 " --> pdb=" O VAL h 517 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG h 522 " --> pdb=" O ASP h 518 " (cutoff:3.500A) 1018 hydrogen bonds defined for protein. 3024 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: 5.83 Time building geometry restraints manager: 4.79 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: 4928 1.34 - 1.46: 3027 1.46 - 1.58: 7133 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 15177 Sorted by residual: bond pdb=" CA TYR h 500 " pdb=" C TYR h 500 " ideal model delta sigma weight residual 1.528 1.492 0.036 1.33e-02 5.65e+03 7.24e+00 bond pdb=" CB ASP m 436 " pdb=" CG ASP m 436 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.29e+00 bond pdb=" CB ASP f 687 " pdb=" CG ASP f 687 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.27e+00 bond pdb=" CB ASP B 113 " pdb=" CG ASP B 113 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.25e+00 bond pdb=" CA ASP h 496 " pdb=" C ASP h 496 " ideal model delta sigma weight residual 1.526 1.502 0.024 1.21e-02 6.83e+03 4.02e+00 ... (remaining 15172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 20094 3.21 - 6.43: 289 6.43 - 9.64: 60 9.64 - 12.85: 23 12.85 - 16.06: 7 Bond angle restraints: 20473 Sorted by residual: angle pdb=" CA GLN C 117 " pdb=" CB GLN C 117 " pdb=" CG GLN C 117 " ideal model delta sigma weight residual 114.10 125.07 -10.97 2.00e+00 2.50e-01 3.01e+01 angle pdb=" CB MET j 364 " pdb=" CG MET j 364 " pdb=" SD MET j 364 " ideal model delta sigma weight residual 112.70 128.58 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" CG1 ILE C 147 " pdb=" CB ILE C 147 " pdb=" CG2 ILE C 147 " ideal model delta sigma weight residual 110.70 95.30 15.40 3.00e+00 1.11e-01 2.63e+01 angle pdb=" CB LYS j 352 " pdb=" CG LYS j 352 " pdb=" CD LYS j 352 " ideal model delta sigma weight residual 111.30 123.03 -11.73 2.30e+00 1.89e-01 2.60e+01 angle pdb=" C LYS m 337 " pdb=" N ASP m 338 " pdb=" CA ASP m 338 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 ... (remaining 20468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 7782 18.01 - 36.01: 1114 36.01 - 54.02: 314 54.02 - 72.02: 68 72.02 - 90.03: 26 Dihedral angle restraints: 9304 sinusoidal: 3948 harmonic: 5356 Sorted by residual: dihedral pdb=" CA PHE f 339 " pdb=" C PHE f 339 " pdb=" N PRO f 340 " pdb=" CA PRO f 340 " ideal model delta harmonic sigma weight residual 180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ALA f 405 " pdb=" C ALA f 405 " pdb=" N TYR f 406 " pdb=" CA TYR f 406 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA TRP h 384 " pdb=" C TRP h 384 " pdb=" N SER h 385 " pdb=" CA SER h 385 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 9301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2193 0.123 - 0.247: 53 0.247 - 0.370: 5 0.370 - 0.493: 0 0.493 - 0.616: 1 Chirality restraints: 2252 Sorted by residual: chirality pdb=" CB VAL f 404 " pdb=" CA VAL f 404 " pdb=" CG1 VAL f 404 " pdb=" CG2 VAL f 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.01 -0.62 2.00e-01 2.50e+01 9.50e+00 chirality pdb=" CG LEU C 115 " pdb=" CB LEU C 115 " pdb=" CD1 LEU C 115 " pdb=" CD2 LEU C 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB ILE C 147 " pdb=" CA ILE C 147 " pdb=" CG1 ILE C 147 " pdb=" CG2 ILE C 147 " both_signs ideal model delta sigma weight residual False 2.64 2.98 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2249 not shown) Planarity restraints: 2658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE m 339 " -0.042 2.00e-02 2.50e+03 8.25e-02 6.80e+01 pdb=" C PHE m 339 " 0.143 2.00e-02 2.50e+03 pdb=" O PHE m 339 " -0.054 2.00e-02 2.50e+03 pdb=" N PRO m 340 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE f 339 " -0.041 2.00e-02 2.50e+03 8.15e-02 6.65e+01 pdb=" C PHE f 339 " 0.141 2.00e-02 2.50e+03 pdb=" O PHE f 339 " -0.053 2.00e-02 2.50e+03 pdb=" N PRO f 340 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP f 546 " 0.026 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP f 546 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP f 546 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP f 546 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP f 546 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP f 546 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP f 546 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 546 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 546 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP f 546 " 0.009 2.00e-02 2.50e+03 ... (remaining 2655 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 20 2.40 - 3.02: 7147 3.02 - 3.65: 24186 3.65 - 4.27: 32042 4.27 - 4.90: 54092 Nonbonded interactions: 117487 Sorted by model distance: nonbonded pdb=" ND2 ASN f 579 " pdb=" ND2 ASN h 497 " model vdw 1.770 3.200 nonbonded pdb=" OG SER h 257 " pdb=" O MET h 310 " model vdw 2.280 3.040 nonbonded pdb=" NH2 ARG f1003 " pdb=" O PHE m 623 " model vdw 2.315 3.120 nonbonded pdb=" O LEU f1033 " pdb=" OG SER f1036 " model vdw 2.317 3.040 nonbonded pdb=" O ASN f1021 " pdb=" OG1 THR f1024 " model vdw 2.320 3.040 ... (remaining 117482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.000 Set scattering table: 0.130 Process input model: 36.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.005 0.054 15177 Z= 0.334 Angle : 1.033 16.063 20473 Z= 0.528 Chirality : 0.052 0.616 2252 Planarity : 0.007 0.082 2658 Dihedral : 18.623 90.028 5802 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.45 % Favored : 97.44 % Rotamer: Outliers : 0.74 % Allowed : 26.63 % Favored : 72.63 % 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: -0.80 (0.18), residues: 1794 helix: -0.04 (0.13), residues: 1171 sheet: -1.27 (0.39), residues: 166 loop : -1.15 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP f 546 HIS 0.007 0.001 HIS B 168 PHE 0.046 0.003 PHE C 111 TYR 0.037 0.002 TYR B 94 ARG 0.011 0.001 ARG f1020 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 230 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 GLU cc_start: 0.8005 (pp20) cc_final: 0.7781 (pp20) REVERT: B 94 TYR cc_start: 0.7749 (t80) cc_final: 0.7410 (t80) REVERT: C 135 GLN cc_start: 0.8568 (pp30) cc_final: 0.8359 (pp30) REVERT: f 246 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: h 388 MET cc_start: 0.7964 (mtp) cc_final: 0.7723 (mtp) REVERT: j 365 LYS cc_start: 0.9188 (ttpp) cc_final: 0.8967 (ttpp) outliers start: 12 outliers final: 2 residues processed: 241 average time/residue: 0.3731 time to fit residues: 126.0586 Evaluate side-chains 199 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 246 GLN Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 495 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN B 87 ASN C 162 ASN ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 246 GLN h 393 GLN h 497 ASN ** h 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 637 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15177 Z= 0.201 Angle : 0.552 9.099 20473 Z= 0.289 Chirality : 0.039 0.187 2252 Planarity : 0.004 0.050 2658 Dihedral : 4.348 32.324 2000 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.77 % Allowed : 24.78 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.20), residues: 1794 helix: 1.63 (0.15), residues: 1178 sheet: -1.11 (0.39), residues: 171 loop : -0.76 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP h 483 HIS 0.004 0.001 HIS B 165 PHE 0.024 0.002 PHE f 409 TYR 0.013 0.001 TYR f 427 ARG 0.006 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 TYR cc_start: 0.7824 (t80) cc_final: 0.7499 (t80) REVERT: C 84 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7428 (mtm110) REVERT: C 135 GLN cc_start: 0.8667 (pp30) cc_final: 0.8307 (pp30) REVERT: f 274 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7560 (tp30) REVERT: f 640 ASP cc_start: 0.8569 (t0) cc_final: 0.8265 (t70) REVERT: f 868 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7603 (ppp) REVERT: h 388 MET cc_start: 0.8002 (mtp) cc_final: 0.7719 (mtp) REVERT: h 595 ILE cc_start: 0.8697 (mt) cc_final: 0.8350 (mt) REVERT: m 195 HIS cc_start: 0.7714 (m90) cc_final: 0.7470 (m90) REVERT: m 336 MET cc_start: 0.7123 (mmm) cc_final: 0.6783 (mmm) REVERT: m 467 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8345 (ttp-170) outliers start: 45 outliers final: 26 residues processed: 252 average time/residue: 0.3374 time to fit residues: 120.1854 Evaluate side-chains 214 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain f residue 274 GLU Chi-restraints excluded: chain f residue 328 THR Chi-restraints excluded: chain f residue 409 PHE Chi-restraints excluded: chain f residue 419 VAL Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 685 ASP Chi-restraints excluded: chain f residue 795 VAL Chi-restraints excluded: chain f residue 849 ASP Chi-restraints excluded: chain f residue 868 MET Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 389 LEU Chi-restraints excluded: chain h residue 403 SER Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 415 VAL Chi-restraints excluded: chain h residue 456 ILE Chi-restraints excluded: chain j residue 349 VAL Chi-restraints excluded: chain m residue 189 LEU Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain m residue 304 LEU Chi-restraints excluded: chain m residue 398 THR Chi-restraints excluded: chain m residue 467 ARG Chi-restraints excluded: chain m residue 665 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 135 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: