Starting phenix.real_space_refine on Sat Aug 3 17:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nur_0520/08_2024/6nur_0520.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nur_0520/08_2024/6nur_0520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nur_0520/08_2024/6nur_0520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nur_0520/08_2024/6nur_0520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nur_0520/08_2024/6nur_0520.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nur_0520/08_2024/6nur_0520.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 Zn 2 6.06 5 S 67 5.16 5 C 5506 2.51 5 N 1451 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8647 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6377 Classifications: {'peptide': 793} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 766} Chain breaks: 1 Chain: "B" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 540 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "D" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1521 SG CYS A 301 40.080 60.791 35.896 1.00 1.02 S ATOM 1562 SG CYS A 306 40.063 59.481 33.140 1.00 0.00 S ATOM 1594 SG CYS A 310 43.007 59.321 35.327 1.00 0.24 S ATOM 3002 SG CYS A 487 22.083 57.548 45.278 1.00 25.56 S ATOM 4255 SG CYS A 645 20.457 57.697 42.141 1.00 16.61 S ATOM 4261 SG CYS A 646 24.056 59.797 43.075 1.00 22.36 S Time building chain proxies: 5.21, per 1000 atoms: 0.60 Number of scatterers: 8647 At special positions: 0 Unit cell: (88.55, 92, 128.8, 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) Zn 2 29.99 S 67 16.00 O 1621 8.00 N 1451 7.00 C 5506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 53.7% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 3.963A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.752A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.841A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.670A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 517 removed outlier: 4.036A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 5.037A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.406A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.817A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.949A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 915 removed outlier: 3.775A pdb=" N THR A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'B' and resid 78 through 99 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.766A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 176 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.625A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY A 203 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.428A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 345 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.827A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.827A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA6, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA7, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.462A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1734 1.32 - 1.45: 2564 1.45 - 1.58: 4414 1.58 - 1.71: 19 1.71 - 1.84: 102 Bond restraints: 8833 Sorted by residual: bond pdb=" NE ARG A 365 " pdb=" CZ ARG A 365 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.67e+01 bond pdb=" CB ASN A 657 " pdb=" CG ASN A 657 " ideal model delta sigma weight residual 1.516 1.417 0.099 2.50e-02 1.60e+03 1.58e+01 bond pdb=" CA PRO A 322 " pdb=" C PRO A 322 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.52e+01 bond pdb=" CB HIS C 36 " pdb=" CG HIS C 36 " ideal model delta sigma weight residual 1.497 1.444 0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" NE1 TRP A 290 " pdb=" CE2 TRP A 290 " ideal model delta sigma weight residual 1.370 1.329 0.041 1.10e-02 8.26e+03 1.39e+01 ... (remaining 8828 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.13: 162 105.13 - 112.39: 4171 112.39 - 119.65: 3384 119.65 - 126.91: 4199 126.91 - 134.17: 82 Bond angle restraints: 11998 Sorted by residual: angle pdb=" CA PHE A 441 " pdb=" CB PHE A 441 " pdb=" CG PHE A 441 " ideal model delta sigma weight residual 113.80 122.17 -8.37 1.00e+00 1.00e+00 7.00e+01 angle pdb=" C PRO A 322 " pdb=" N PRO A 323 " pdb=" CA PRO A 323 " ideal model delta sigma weight residual 119.56 127.70 -8.14 1.01e+00 9.80e-01 6.50e+01 angle pdb=" C ASN A 168 " pdb=" N PRO A 169 " pdb=" CA PRO A 169 " ideal model delta sigma weight residual 119.82 127.15 -7.33 9.80e-01 1.04e+00 5.59e+01 angle pdb=" N ILE A 757 " pdb=" CA ILE A 757 " pdb=" C ILE A 757 " ideal model delta sigma weight residual 108.11 118.50 -10.39 1.40e+00 5.10e-01 5.51e+01 angle pdb=" CA ASP A 846 " pdb=" CB ASP A 846 " pdb=" CG ASP A 846 " ideal model delta sigma weight residual 112.60 119.89 -7.29 1.00e+00 1.00e+00 5.31e+01 ... (remaining 11993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5067 17.30 - 34.60: 150 34.60 - 51.89: 29 51.89 - 69.19: 23 69.19 - 86.49: 5 Dihedral angle restraints: 5274 sinusoidal: 2054 harmonic: 3220 Sorted by residual: dihedral pdb=" C PHE A 441 " pdb=" N PHE A 441 " pdb=" CA PHE A 441 " pdb=" CB PHE A 441 " ideal model delta harmonic sigma weight residual -122.60 -113.94 -8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" C PHE D 92 " pdb=" N PHE D 92 " pdb=" CA PHE D 92 " pdb=" CB PHE D 92 " ideal model delta harmonic sigma weight residual -122.60 -131.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" CG ARG A 583 " pdb=" CD ARG A 583 " pdb=" NE ARG A 583 " pdb=" CZ ARG A 583 " ideal model delta sinusoidal sigma weight residual 90.00 44.09 45.91 2 1.50e+01 4.44e-03 1.10e+01 ... (remaining 5271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 782 0.070 - 0.140: 405 0.140 - 0.210: 128 0.210 - 0.279: 33 0.279 - 0.349: 8 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA MET A 242 " pdb=" N MET A 242 " pdb=" C MET A 242 " pdb=" CB MET A 242 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA PHE D 92 " pdb=" N PHE D 92 " pdb=" C PHE D 92 " pdb=" CB PHE D 92 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU A 136 " pdb=" N GLU A 136 " pdb=" C GLU A 136 " pdb=" CB GLU A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1353 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 546 " 0.067 2.00e-02 2.50e+03 3.55e-02 2.52e+01 pdb=" CG TYR A 546 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 546 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 546 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 546 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 546 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 546 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 546 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 515 " -0.057 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR A 515 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 515 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 515 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 515 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 515 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 515 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 515 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 217 " -0.049 2.00e-02 2.50e+03 2.86e-02 1.63e+01 pdb=" CG TYR A 217 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 217 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 217 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 217 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 217 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 217 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 217 " -0.050 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2254 2.80 - 3.32: 8108 3.32 - 3.85: 14981 3.85 - 4.37: 18295 4.37 - 4.90: 29735 Nonbonded interactions: 73373 Sorted by model distance: nonbonded pdb=" O CYS A 645 " pdb="ZN ZN A1002 " model vdw 2.270 2.230 nonbonded pdb=" OD2 ASP C 5 " pdb=" NZ LYS D 97 " model vdw 2.354 3.120 nonbonded pdb=" O ARG A 733 " pdb=" C ASN A 734 " model vdw 2.366 3.270 nonbonded pdb=" OD2 ASP A 258 " pdb=" NZ LYS A 263 " model vdw 2.422 3.120 nonbonded pdb=" N ASP B 112 " pdb=" OD1 ASP B 112 " model vdw 2.424 3.120 ... (remaining 73368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 84 through 191) selection = (chain 'D' and resid 84 through 191) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.740 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.016 0.111 8833 Z= 1.012 Angle : 1.552 10.388 11998 Z= 1.078 Chirality : 0.092 0.349 1356 Planarity : 0.008 0.038 1537 Dihedral : 10.589 86.487 3192 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.52 % Allowed : 0.73 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1077 helix: -0.42 (0.20), residues: 478 sheet: 0.74 (0.47), residues: 98 loop : 0.33 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.009 TRP A 509 HIS 0.014 0.002 HIS A 613 PHE 0.037 0.006 PHE A 441 TYR 0.067 0.008 TYR A 546 ARG 0.008 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 285 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 138 ASN cc_start: 0.7938 (m-40) cc_final: 0.7552 (m-40) REVERT: A 183 ARG cc_start: 0.8177 (ptm-80) cc_final: 0.7717 (ttt-90) REVERT: A 583 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8317 (mtt90) REVERT: A 733 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.6901 (mmt180) REVERT: A 739 HIS cc_start: 0.8393 (m-70) cc_final: 0.8054 (m90) REVERT: C 25 SER cc_start: 0.7705 (t) cc_final: 0.7490 (p) outliers start: 5 outliers final: 2 residues processed: 290 average time/residue: 0.2368 time to fit residues: 90.1565 Evaluate side-chains 175 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 785 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.259 > 50: distance: 22 - 34: 3.096 distance: 47 - 52: 33.390 distance: 52 - 53: 38.557 distance: 53 - 54: 41.401 distance: 54 - 56: 55.904 distance: 56 - 57: 8.875 distance: 57 - 58: 30.750 distance: 57 - 60: 52.630 distance: 58 - 59: 10.090 distance: 58 - 70: 22.917 distance: 60 - 61: 27.493 distance: 61 - 62: 7.138 distance: 61 - 63: 16.856 distance: 62 - 64: 12.691 distance: 63 - 65: 16.194 distance: 64 - 65: 13.808 distance: 65 - 67: 14.800 distance: 66 - 68: 7.882 distance: 67 - 69: 19.641 distance: 68 - 69: 17.909 distance: 70 - 71: 18.979 distance: 71 - 72: 33.038 distance: 71 - 74: 13.012 distance: 72 - 73: 47.127 distance: 72 - 78: 17.518 distance: 74 - 75: 10.114 distance: 75 - 76: 27.068 distance: 75 - 77: 9.599 distance: 78 - 79: 27.919 distance: 79 - 80: 41.727 distance: 79 - 82: 62.332 distance: 80 - 81: 49.175 distance: 80 - 90: 26.268 distance: 82 - 83: 15.621 distance: 83 - 84: 11.698 distance: 83 - 85: 8.509 distance: 84 - 86: 17.788 distance: 85 - 87: 5.956 distance: 87 - 88: 19.861 distance: 88 - 89: 8.759 distance: 90 - 91: 56.038 distance: 90 - 96: 42.034 distance: 91 - 92: 53.595 distance: 91 - 94: 42.218 distance: 92 - 93: 32.182 distance: 92 - 97: 36.297 distance: 94 - 95: 5.646 distance: 95 - 96: 57.790 distance: 97 - 98: 26.950 distance: 98 - 99: 28.519 distance: 98 - 101: 21.667 distance: 99 - 100: 15.428 distance: 99 - 106: 37.066 distance: 100 - 131: 29.655 distance: 101 - 102: 16.535 distance: 102 - 103: 10.097 distance: 103 - 104: 5.473 distance: 104 - 105: 3.231 distance: 106 - 107: 53.198 distance: 107 - 108: 48.117 distance: 107 - 110: 36.882 distance: 108 - 109: 50.645 distance: 108 - 112: 35.761 distance: 109 - 136: 37.471 distance: 110 - 111: 43.207 distance: 112 - 113: 21.736 distance: 113 - 114: 34.781 distance: 113 - 116: 62.063 distance: 114 - 115: 56.527 distance: 114 - 120: 51.781 distance: 116 - 117: 12.997 distance: 117 - 118: 46.603 distance: 117 - 119: 39.554 distance: 120 - 121: 33.569 distance: 121 - 122: 41.102 distance: 121 - 124: 22.089 distance: 122 - 123: 47.578 distance: 122 - 131: 47.791 distance: 124 - 125: 42.784 distance: 125 - 126: 28.587 distance: 126 - 127: 8.463 distance: 127 - 128: 6.907 distance: 128 - 130: 11.048 distance: 131 - 132: 50.711 distance: 132 - 133: 34.418 distance: 132 - 135: 27.018 distance: 133 - 134: 16.066 distance: 133 - 136: 31.783 distance: 167 - 178: 3.007