Starting phenix.real_space_refine on Sat Jun 14 00:17:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rkv_4912/06_2025/6rkv_4912.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rkv_4912/06_2025/6rkv_4912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rkv_4912/06_2025/6rkv_4912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rkv_4912/06_2025/6rkv_4912.map" model { file = "/net/cci-nas-00/data/ceres_data/6rkv_4912/06_2025/6rkv_4912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rkv_4912/06_2025/6rkv_4912.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 54 5.16 5 C 9522 2.51 5 N 2750 2.21 5 O 3070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15460 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "B" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "C" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "D" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "F" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 9.41, per 1000 atoms: 0.61 Number of scatterers: 15460 At special positions: 0 Unit cell: (122.32, 146.96, 123.2, 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 54 16.00 P 64 15.00 O 3070 8.00 N 2750 7.00 C 9522 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: 3.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 22 sheets defined 50.0% alpha, 10.4% beta 32 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.934A pdb=" N SER A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 95 through 98 removed outlier: 3.635A pdb=" N LEU A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.604A pdb=" N HIS A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 removed outlier: 4.451A pdb=" N ILE A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 346 through 389 removed outlier: 3.518A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.765A pdb=" N LYS A 465 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 494 Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.931A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 4.415A pdb=" N SER B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.023A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 602 through 609 removed outlier: 4.061A pdb=" N LEU B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.670A pdb=" N SER B 621 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 641 removed outlier: 3.680A pdb=" N VAL B 626 " --> pdb=" O ASP B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 718 through 732 Processing helix chain 'B' and resid 741 through 745 removed outlier: 4.242A pdb=" N MET B 745 " --> pdb=" O LEU B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 772 through 778 removed outlier: 4.205A pdb=" N THR B 778 " --> pdb=" O ASP B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 786 Processing helix chain 'C' and resid 15 through 32 removed outlier: 3.933A pdb=" N SER C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 95 through 98 removed outlier: 3.636A pdb=" N LEU C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.605A pdb=" N HIS C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 removed outlier: 4.451A pdb=" N ILE C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 346 through 389 removed outlier: 3.518A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.765A pdb=" N LYS C 465 " --> pdb=" O ARG C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 494 Processing helix chain 'C' and resid 494 through 513 removed outlier: 3.931A pdb=" N LEU C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 removed outlier: 4.415A pdb=" N SER D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 524 removed outlier: 4.023A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 602 through 609 removed outlier: 4.061A pdb=" N LEU D 606 " --> pdb=" O PRO D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 621 removed outlier: 3.669A pdb=" N SER D 621 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 641 removed outlier: 3.680A pdb=" N VAL D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 684 through 699 Processing helix chain 'D' and resid 718 through 732 Processing helix chain 'D' and resid 741 through 745 removed outlier: 4.241A pdb=" N MET D 745 " --> pdb=" O LEU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 772 through 778 removed outlier: 4.205A pdb=" N THR D 778 " --> pdb=" O ASP D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 786 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.702A pdb=" N LYS A 64 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.730A pdb=" N GLY A 238 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 250 removed outlier: 6.961A pdb=" N ARG A 245 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 247 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 291 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.827A pdb=" N ALA A 336 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 441 through 446 removed outlier: 6.158A pdb=" N GLU B 419 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 444 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR B 421 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B 446 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 423 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AB1, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.664A pdb=" N THR B 565 " --> pdb=" O GLU B 708 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 708 " --> pdb=" O THR B 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 653 removed outlier: 3.537A pdb=" N VAL B 664 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.701A pdb=" N LYS C 64 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 174 Processing sheet with id=AB6, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AB7, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.730A pdb=" N GLY C 238 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.960A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 247 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA C 291 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 335 through 337 removed outlier: 3.828A pdb=" N ALA C 336 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 441 through 446 removed outlier: 6.158A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 446 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL D 423 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AC3, first strand: chain 'D' and resid 565 through 566 removed outlier: 3.664A pdb=" N THR D 565 " --> pdb=" O GLU D 708 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 708 " --> pdb=" O THR D 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 653 removed outlier: 3.536A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 4.36 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: 4540 1.34 - 1.45: 2427 1.45 - 1.57: 8655 1.57 - 1.69: 124 1.69 - 1.81: 102 Bond restraints: 15848 Sorted by residual: bond pdb=" C ASN D 484 " pdb=" N PRO D 485 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.11e+00 bond pdb=" C ASN B 484 " pdb=" N PRO B 485 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.07e+00 bond pdb=" CA ASN D 484 " pdb=" C ASN D 484 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.60e-01 bond pdb=" CA ASN B 484 " pdb=" C ASN B 484 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.50e-01 bond pdb=" CA ASP C 391 " pdb=" C ASP C 391 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.60e-01 ... (remaining 15843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 21324 1.76 - 3.53: 322 3.53 - 5.29: 29 5.29 - 7.06: 11 7.06 - 8.82: 6 Bond angle restraints: 21692 Sorted by residual: angle pdb=" N GLY D 577 " pdb=" CA GLY D 577 " pdb=" C GLY D 577 " ideal model delta sigma weight residual 111.56 115.47 -3.91 1.01e+00 9.80e-01 1.50e+01 angle pdb=" N GLY B 577 " pdb=" CA GLY B 577 " pdb=" C GLY B 577 " ideal model delta sigma weight residual 111.56 115.45 -3.89 1.01e+00 9.80e-01 1.48e+01 angle pdb=" C THR D 779 " pdb=" N LEU D 780 " pdb=" CA LEU D 780 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C THR B 779 " pdb=" N LEU B 780 " pdb=" CA LEU B 780 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N ASN D 484 " pdb=" CA ASN D 484 " pdb=" C ASN D 484 " ideal model delta sigma weight residual 109.81 117.41 -7.60 2.21e+00 2.05e-01 1.18e+01 ... (remaining 21687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 9148 28.11 - 56.23: 366 56.23 - 84.34: 34 84.34 - 112.45: 0 112.45 - 140.56: 4 Dihedral angle restraints: 9552 sinusoidal: 4376 harmonic: 5176 Sorted by residual: dihedral pdb=" CA ALA D 655 " pdb=" C ALA D 655 " pdb=" N GLU D 656 " pdb=" CA GLU D 656 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ALA B 655 " pdb=" C ALA B 655 " pdb=" N GLU B 656 " pdb=" CA GLU B 656 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" C4' DT H 26 " pdb=" C3' DT H 26 " pdb=" O3' DT H 26 " pdb=" P DT H 27 " ideal model delta sinusoidal sigma weight residual 220.00 79.44 140.56 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 9549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1879 0.040 - 0.080: 427 0.080 - 0.121: 136 0.121 - 0.161: 0 0.161 - 0.201: 2 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CA ASN D 484 " pdb=" N ASN D 484 " pdb=" C ASN D 484 " pdb=" CB ASN D 484 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASN B 484 " pdb=" N ASN B 484 " pdb=" C ASN B 484 " pdb=" CB ASN B 484 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE B 450 " pdb=" N ILE B 450 " pdb=" C ILE B 450 " pdb=" CB ILE B 450 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 2441 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 780 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C LEU B 780 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU B 780 " -0.020 2.00e-02 2.50e+03 pdb=" N MET B 781 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 780 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.74e+00 pdb=" C LEU D 780 " -0.054 2.00e-02 2.50e+03 pdb=" O LEU D 780 " 0.020 2.00e-02 2.50e+03 pdb=" N MET D 781 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 182 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 183 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.023 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2771 2.78 - 3.31: 14085 3.31 - 3.84: 23957 3.84 - 4.37: 25913 4.37 - 4.90: 44911 Nonbonded interactions: 111637 Sorted by model distance: nonbonded pdb=" OE2 GLU D 454 " pdb=" NH1 ARG D 516 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU B 454 " pdb=" NH1 ARG B 516 " model vdw 2.247 3.120 nonbonded pdb=" OD2 ASP A 39 " pdb=" NH2 ARG A 46 " model vdw 2.259 3.120 nonbonded pdb=" OD2 ASP C 39 " pdb=" NH2 ARG C 46 " model vdw 2.259 3.120 nonbonded pdb=" O LYS B 538 " pdb=" OG SER B 735 " model vdw 2.282 3.040 ... (remaining 111632 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: 0.08 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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: 2.970 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: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 39.460 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.002 0.025 15848 Z= 0.112 Angle : 0.534 8.819 21692 Z= 0.309 Chirality : 0.037 0.201 2444 Planarity : 0.005 0.041 2610 Dihedral : 13.181 140.565 6212 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.19), residues: 1764 helix: 0.55 (0.17), residues: 836 sheet: -1.81 (0.35), residues: 210 loop : -3.10 (0.20), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 415 HIS 0.005 0.001 HIS A 399 PHE 0.013 0.001 PHE B 514 TYR 0.011 0.001 TYR A 266 ARG 0.002 0.000 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.16646 ( 770) hydrogen bonds : angle 5.39648 ( 2148) covalent geometry : bond 0.00202 (15848) covalent geometry : angle 0.53374 (21692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0143 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0147 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 65 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9127 (tttp) cc_final: 0.8838 (tptp) REVERT: B 660 PHE cc_start: 0.8181 (m-10) cc_final: 0.7574 (m-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2551 time to fit residues: 18.6210 Evaluate side-chains 31 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.348 Evaluate side-chains 92 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.439 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: A 113 ASP cc_start: 0.8785 (m-30) cc_final: 0.7539 (p0) REVERT: A 306 GLU cc_start: 0.8142 (tt0) cc_final: 0.7845 (tm-30) REVERT: A 307 VAL cc_start: 0.9030 (t) cc_final: 0.8790 (t) REVERT: A 326 LEU cc_start: 0.9131 (mt) cc_final: 0.8800 (tt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2172 time to fit residues: 23.5790 Evaluate side-chains 42 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.5980 chunk 137 optimal weight: 0.0670 chunk 76 optimal weight: 0.0470 chunk 47 optimal weight: 0.1980 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 0.0010 chunk 165 optimal weight: 8.9990 overall best weight: 0.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 224 ASN A 357 HIS A 378 HIS A 399 HIS A 456 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057184 restraints weight = 4140.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057639 restraints weight = 1031.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057841 restraints weight = 531.605| |-----------------------------------------------------------------------------| r_work (final): 0.2905 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063294 restraints weight = 5276.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.064634 restraints weight = 1935.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065224 restraints weight = 1162.564| |-----------------------------------------------------------------------------| r_work (final): 0.3184 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.056266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046210 restraints weight = 27613.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.047159 restraints weight = 21184.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.047940 restraints weight = 17195.368| |-----------------------------------------------------------------------------| r_work (final): 0.3195 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.044673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.037850 restraints weight = 34064.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.038884 restraints weight = 21008.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.039669 restraints weight = 14788.866| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15848 Z= 0.125 Angle : 0.582 7.778 21692 Z= 0.303 Chirality : 0.040 0.193 2444 Planarity : 0.005 0.048 2610 Dihedral : 16.973 141.111 2668 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.77 (0.20), residues: 1764 helix: 1.73 (0.18), residues: 824 sheet: -1.54 (0.36), residues: 208 loop : -3.02 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 415 HIS 0.004 0.001 HIS A 399 PHE 0.004 0.001 PHE D 649 TYR 0.015 0.001 TYR C 478 ARG 0.011 0.001 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.06934 ( 770) hydrogen bonds : angle 4.75934 ( 2148) covalent geometry : bond 0.00258 (15848) covalent geometry : angle 0.58250 (21692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0138 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0150 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 Evaluate side-chains 35 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9189 (tttp) cc_final: 0.8873 (tptp) REVERT: B 535 TYR cc_start: 0.8478 (m-10) cc_final: 0.8046 (m-10) REVERT: B 583 LEU cc_start: 0.8778 (mm) cc_final: 0.8331 (pp) REVERT: B 660 PHE cc_start: 0.7982 (m-10) cc_final: 0.7752 (m-10) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2340 time to fit residues: 9.6767 Evaluate side-chains 25 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.388 Evaluate side-chains 51 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.502 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: A 104 ASP cc_start: 0.9330 (t0) cc_final: 0.9019 (t0) REVERT: A 113 ASP cc_start: 0.8901 (m-30) cc_final: 0.7990 (p0) REVERT: A 375 ASP cc_start: 0.9411 (m-30) cc_final: 0.9210 (m-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2058 time to fit residues: 12.9286 Evaluate side-chains 35 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 123 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.2760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056674 restraints weight = 4212.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057067 restraints weight = 983.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057275 restraints weight = 533.711| |-----------------------------------------------------------------------------| r_work (final): 0.3123 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.062228 restraints weight = 5292.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063632 restraints weight = 2177.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064265 restraints weight = 1422.296| |-----------------------------------------------------------------------------| r_work (final): 0.3176 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.054747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.045521 restraints weight = 27937.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.046379 restraints weight = 21950.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047066 restraints weight = 17995.462| |-----------------------------------------------------------------------------| r_work (final): 0.3178 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.042991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036255 restraints weight = 35815.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.037272 restraints weight = 21965.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.038002 restraints weight = 15372.184| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15848 Z= 0.159 Angle : 0.737 10.175 21692 Z= 0.393 Chirality : 0.059 0.922 2444 Planarity : 0.011 0.289 2610 Dihedral : 17.047 142.072 2668 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.53 % Allowed : 3.05 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.16 (0.20), residues: 1764 helix: 1.09 (0.18), residues: 826 sheet: -1.05 (0.38), residues: 186 loop : -2.98 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 629 HIS 0.024 0.002 HIS A 357 PHE 0.010 0.001 PHE C 96 TYR 0.090 0.003 TYR C 63 ARG 0.022 0.001 ARG C 359 Details of bonding type rmsd hydrogen bonds : bond 0.07007 ( 770) hydrogen bonds : angle 4.97189 ( 2148) covalent geometry : bond 0.00350 (15848) covalent geometry : angle 0.73723 (21692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0166 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0162 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Evaluate side-chains 27 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9141 (tttp) cc_final: 0.8849 (tptp) REVERT: B 461 MET cc_start: 0.7301 (mtm) cc_final: 0.7098 (mtm) REVERT: B 535 TYR cc_start: 0.8233 (m-10) cc_final: 0.7840 (m-10) REVERT: B 583 LEU cc_start: 0.8655 (mm) cc_final: 0.8174 (pp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1922 time to fit residues: 6.5532 Evaluate side-chains 22 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.400 Evaluate side-chains 50 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 GLN cc_start: 0.9394 (mt0) cc_final: 0.9121 (mp10) REVERT: C 104 ASP cc_start: 0.9197 (t0) cc_final: 0.8979 (t0) REVERT: C 113 ASP cc_start: 0.8845 (m-30) cc_final: 0.7821 (p0) REVERT: C 375 ASP cc_start: 0.9391 (m-30) cc_final: 0.9170 (m-30) REVERT: C 507 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8987 (tp30) outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 0.2140 time to fit residues: 12.7412 Evaluate side-chains 36 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 136 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 123 optimal weight: 0.0000 chunk 156 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056671 restraints weight = 4268.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057072 restraints weight = 992.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.057266 restraints weight = 542.411| |-----------------------------------------------------------------------------| r_work (final): 0.3123 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.062197 restraints weight = 5398.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063622 restraints weight = 2194.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064270 restraints weight = 1425.010| |-----------------------------------------------------------------------------| r_work (final): 0.3176 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.054517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.045562 restraints weight = 27883.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046388 restraints weight = 22023.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.047048 restraints weight = 18211.059| |-----------------------------------------------------------------------------| r_work (final): 0.3179 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.043089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.036442 restraints weight = 34646.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.037465 restraints weight = 21823.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.038231 restraints weight = 15367.492| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15848 Z= 0.159 Angle : 0.737 10.175 21692 Z= 0.393 Chirality : 0.059 0.922 2444 Planarity : 0.011 0.289 2610 Dihedral : 17.047 142.072 2668 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.16 (0.20), residues: 1764 helix: 1.09 (0.18), residues: 826 sheet: -1.05 (0.38), residues: 186 loop : -2.98 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 629 HIS 0.024 0.002 HIS C 357 PHE 0.010 0.001 PHE C 96 TYR 0.090 0.003 TYR C 63 ARG 0.022 0.001 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.07007 ( 770) hydrogen bonds : angle 4.97189 ( 2148) covalent geometry : bond 0.00351 (15848) covalent geometry : angle 0.73742 (21692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0137 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0175 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 25 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9138 (tttp) cc_final: 0.8839 (tptp) REVERT: B 535 TYR cc_start: 0.8241 (m-10) cc_final: 0.7840 (m-10) REVERT: B 583 LEU cc_start: 0.8656 (mm) cc_final: 0.8175 (pp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1259 time to fit residues: 4.1971 Evaluate side-chains 22 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.324 Evaluate side-chains 34 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9230 (t0) cc_final: 0.8987 (t0) REVERT: A 113 ASP cc_start: 0.8898 (m-30) cc_final: 0.8220 (p0) REVERT: A 375 ASP cc_start: 0.9339 (m-30) cc_final: 0.9128 (m-30) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1604 time to fit residues: 7.0972 Evaluate side-chains 28 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 124 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 32 optimal weight: 0.0870 chunk 98 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056669 restraints weight = 4270.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057064 restraints weight = 991.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057270 restraints weight = 535.144| |-----------------------------------------------------------------------------| r_work (final): 0.3122 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062195 restraints weight = 5434.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063608 restraints weight = 2206.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064243 restraints weight = 1436.976| |-----------------------------------------------------------------------------| r_work (final): 0.3176 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.054522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.045619 restraints weight = 27696.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.046416 restraints weight = 21867.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.047070 restraints weight = 18133.526| |-----------------------------------------------------------------------------| r_work (final): 0.3179 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.043162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.036513 restraints weight = 34741.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.037516 restraints weight = 21951.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.038270 restraints weight = 15521.581| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15848 Z= 0.159 Angle : 0.737 10.172 21692 Z= 0.393 Chirality : 0.059 0.922 2444 Planarity : 0.011 0.289 2610 Dihedral : 17.047 142.072 2668 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.16 (0.20), residues: 1764 helix: 1.09 (0.18), residues: 826 sheet: -1.05 (0.38), residues: 186 loop : -2.98 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 629 HIS 0.024 0.002 HIS C 357 PHE 0.011 0.001 PHE C 96 TYR 0.090 0.003 TYR C 63 ARG 0.022 0.001 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.07007 ( 770) hydrogen bonds : angle 4.97189 ( 2148) covalent geometry : bond 0.00351 (15848) covalent geometry : angle 0.73738 (21692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0146 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0179 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 Evaluate side-chains 25 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9136 (tttp) cc_final: 0.8838 (tptp) REVERT: B 535 TYR cc_start: 0.8239 (m-10) cc_final: 0.7839 (m-10) REVERT: B 583 LEU cc_start: 0.8657 (mm) cc_final: 0.8176 (pp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1614 time to fit residues: 5.3153 Evaluate side-chains 22 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.570 Evaluate side-chains 31 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9239 (t0) cc_final: 0.8992 (t0) REVERT: A 113 ASP cc_start: 0.8890 (m-30) cc_final: 0.8218 (p0) REVERT: A 375 ASP cc_start: 0.9343 (m-30) cc_final: 0.9131 (m-30) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2095 time to fit residues: 8.5632 Evaluate side-chains 28 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 166 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 155 optimal weight: 0.0370 chunk 63 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056685 restraints weight = 4019.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057133 restraints weight = 963.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057333 restraints weight = 508.405| |-----------------------------------------------------------------------------| r_work (final): 0.3126 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062178 restraints weight = 5484.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063616 restraints weight = 2215.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064239 restraints weight = 1434.085| |-----------------------------------------------------------------------------| r_work (final): 0.3176 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.054524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.045592 restraints weight = 27903.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.046394 restraints weight = 22009.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.047063 restraints weight = 18190.438| |-----------------------------------------------------------------------------| r_work (final): 0.3179 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.043170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.036491 restraints weight = 34816.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.037519 restraints weight = 22125.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.038271 restraints weight = 15587.847| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15848 Z= 0.158 Angle : 0.736 10.053 21692 Z= 0.392 Chirality : 0.059 0.906 2444 Planarity : 0.011 0.288 2610 Dihedral : 17.047 142.072 2668 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.17 (0.20), residues: 1764 helix: 1.09 (0.18), residues: 826 sheet: -1.05 (0.38), residues: 186 loop : -2.98 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 629 HIS 0.024 0.002 HIS A 357 PHE 0.011 0.001 PHE C 96 TYR 0.089 0.003 TYR C 63 ARG 0.022 0.001 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.07008 ( 770) hydrogen bonds : angle 4.97189 ( 2148) covalent geometry : bond 0.00351 (15848) covalent geometry : angle 0.73554 (21692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0128 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0186 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 25 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9138 (tttp) cc_final: 0.8839 (tptp) REVERT: B 535 TYR cc_start: 0.8247 (m-10) cc_final: 0.7846 (m-10) REVERT: B 583 LEU cc_start: 0.8659 (mm) cc_final: 0.8178 (pp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1407 time to fit residues: 4.7922 Evaluate side-chains 22 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.353 Evaluate side-chains 31 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9237 (t0) cc_final: 0.8992 (t0) REVERT: A 113 ASP cc_start: 0.8894 (m-30) cc_final: 0.8221 (p0) REVERT: A 375 ASP cc_start: 0.9341 (m-30) cc_final: 0.9129 (m-30) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1788 time to fit residues: 7.4074 Evaluate side-chains 28 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 120 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.058530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.056482 restraints weight = 4269.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.056895 restraints weight = 1014.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057145 restraints weight = 532.522| |-----------------------------------------------------------------------------| r_work (final): 0.2884 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.067675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.061479 restraints weight = 5204.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062864 restraints weight = 2268.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.063456 restraints weight = 1447.009| |-----------------------------------------------------------------------------| r_work (final): 0.3160 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.053382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044545 restraints weight = 28793.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.045327 restraints weight = 22567.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.045803 restraints weight = 18779.221| |-----------------------------------------------------------------------------| r_work (final): 0.3143 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.042432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.035806 restraints weight = 35650.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.036805 restraints weight = 22501.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.037530 restraints weight = 16002.825| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 15848 Z= 0.231 Angle : 0.753 8.400 21692 Z= 0.401 Chirality : 0.046 0.294 2444 Planarity : 0.008 0.123 2610 Dihedral : 17.032 142.589 2668 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.53 (0.20), residues: 1764 helix: 0.72 (0.18), residues: 826 sheet: -1.14 (0.38), residues: 186 loop : -3.10 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 629 HIS 0.024 0.002 HIS C 357 PHE 0.016 0.002 PHE C 96 TYR 0.090 0.004 TYR A 63 ARG 0.030 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.06962 ( 770) hydrogen bonds : angle 5.08334 ( 2148) covalent geometry : bond 0.00502 (15848) covalent geometry : angle 0.75275 (21692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0246 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0162 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Evaluate side-chains 25 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9130 (tttp) cc_final: 0.8818 (tptp) REVERT: B 461 MET cc_start: 0.7550 (mtm) cc_final: 0.7342 (mtm) REVERT: B 535 TYR cc_start: 0.8251 (m-10) cc_final: 0.7889 (m-10) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1566 time to fit residues: 5.1831 Evaluate side-chains 22 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.390 Evaluate side-chains 31 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9234 (t0) cc_final: 0.8975 (t0) REVERT: A 375 ASP cc_start: 0.9366 (m-30) cc_final: 0.9166 (m-30) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1723 time to fit residues: 7.0720 Evaluate side-chains 25 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.3679 > 50: distance: 0 - 1: 5.235 distance: 1 - 4: 5.820 distance: 2 - 3: 14.648 distance: 2 - 11: 14.211 distance: 4 - 5: 4.816 distance: 5 - 7: 4.850 distance: 7 - 9: 4.121 distance: 9 - 10: 3.405 distance: 11 - 12: 8.069 distance: 12 - 13: 8.795 distance: 12 - 15: 16.224 distance: 13 - 14: 26.946 distance: 13 - 18: 14.558 distance: 15 - 16: 7.033 distance: 16 - 17: 19.579 distance: 18 - 19: 22.254 distance: 19 - 20: 10.461 distance: 19 - 22: 17.023 distance: 20 - 21: 6.890 distance: 20 - 25: 6.464 distance: 22 - 23: 17.775 distance: 22 - 24: 16.326 distance: 25 - 26: 7.074 distance: 26 - 27: 6.627 distance: 26 - 29: 8.363 distance: 27 - 28: 30.950 distance: 27 - 30: 23.738 distance: 30 - 31: 20.340 distance: 31 - 32: 6.276 distance: 31 - 34: 24.075 distance: 32 - 33: 7.250 distance: 32 - 35: 9.714 distance: 35 - 36: 6.153 distance: 36 - 37: 12.952 distance: 36 - 39: 6.030 distance: 37 - 38: 21.270 distance: 37 - 43: 19.365 distance: 39 - 40: 12.196 distance: 39 - 41: 6.085 distance: 40 - 42: 11.880 distance: 43 - 44: 11.832 distance: 44 - 45: 8.173 distance: 44 - 47: 6.770 distance: 45 - 46: 20.469 distance: 45 - 51: 25.587 distance: 47 - 48: 5.600 distance: 47 - 49: 7.577 distance: 48 - 50: 11.271 distance: 51 - 52: 26.954 distance: 52 - 53: 5.356 distance: 52 - 55: 14.523 distance: 53 - 54: 7.001 distance: 53 - 59: 11.753 distance: 56 - 57: 18.271 distance: 56 - 58: 16.189 distance: 59 - 60: 14.064 distance: 60 - 61: 20.917 distance: 61 - 62: 25.317 distance: 61 - 63: 27.862 distance: 63 - 64: 10.703 distance: 64 - 65: 7.251 distance: 64 - 67: 16.775 distance: 65 - 66: 7.591 distance: 67 - 68: 5.097 distance: 68 - 69: 3.299 distance: 69 - 70: 3.281