Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:01:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/12_2022/6vef_21156_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/12_2022/6vef_21156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/12_2022/6vef_21156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/12_2022/6vef_21156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/12_2022/6vef_21156_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vef_21156/12_2022/6vef_21156_updated_updated.pdb" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ARG 612": "NH1" <-> "NH2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 900": "NH1" <-> "NH2" Residue "A ARG 904": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B ARG 612": "NH1" <-> "NH2" Residue "B ARG 763": "NH1" <-> "NH2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 783": "NH1" <-> "NH2" Residue "B ARG 900": "NH1" <-> "NH2" Residue "B ARG 904": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6675 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 39, 'TRANS': 804} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6675 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 39, 'TRANS': 804} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'OAA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'OAA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Time building chain proxies: 7.63, per 1000 atoms: 0.57 Number of scatterers: 13414 At special positions: 0 Unit cell: (116.641, 106.117, 127.165, 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 66 16.00 P 2 15.00 O 2512 8.00 N 2400 7.00 C 8434 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: 5.87 Conformation dependent library (CDL) restraints added in 2.8 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 10 sheets defined 34.6% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 86 through 101 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 365 through 374 removed outlier: 4.658A pdb=" N LYS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 532 through 535 Proline residue: A 535 - end of helix No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 593 through 607 removed outlier: 3.536A pdb=" N ASP A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 672 Processing helix chain 'A' and resid 688 through 691 Processing helix chain 'A' and resid 695 through 699 Processing helix chain 'A' and resid 704 through 707 No H-bonds generated for 'chain 'A' and resid 704 through 707' Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 754 through 765 Processing helix chain 'A' and resid 780 through 783 removed outlier: 3.605A pdb=" N ARG A 783 " --> pdb=" O SER A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 780 through 783' Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 823 through 832 Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 885 through 892 removed outlier: 5.009A pdb=" N ARG A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 929 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 197 through 220 Processing helix chain 'B' and resid 234 through 248 Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 365 through 374 removed outlier: 4.658A pdb=" N LYS B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 532 through 535 Proline residue: B 535 - end of helix No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 593 through 607 removed outlier: 3.536A pdb=" N ASP B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 607 " --> pdb=" O THR B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 672 Processing helix chain 'B' and resid 688 through 691 Processing helix chain 'B' and resid 695 through 699 Processing helix chain 'B' and resid 704 through 707 No H-bonds generated for 'chain 'B' and resid 704 through 707' Processing helix chain 'B' and resid 735 through 737 No H-bonds generated for 'chain 'B' and resid 735 through 737' Processing helix chain 'B' and resid 754 through 765 Processing helix chain 'B' and resid 780 through 783 removed outlier: 3.605A pdb=" N ARG B 783 " --> pdb=" O SER B 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 780 through 783' Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 823 through 832 Processing helix chain 'B' and resid 853 through 858 Processing helix chain 'B' and resid 885 through 892 removed outlier: 5.009A pdb=" N ARG B 890 " --> pdb=" O GLN B 886 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU B 891 " --> pdb=" O HIS B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 929 Processing sheet with id= A, first strand: chain 'A' and resid 168 through 171 Processing sheet with id= B, first strand: chain 'A' and resid 253 through 258 removed outlier: 6.891A pdb=" N VAL A 384 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N HIS A 355 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 386 " --> pdb=" O HIS A 355 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL A 448 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL A 387 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A 450 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN A 389 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 452 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 301 through 306 Processing sheet with id= D, first strand: chain 'A' and resid 611 through 613 removed outlier: 6.243A pdb=" N LEU A 679 " --> pdb=" O ARG A 612 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL A 715 " --> pdb=" O TRP A 682 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU A 773 " --> pdb=" O MET A 716 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU A 718 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL A 775 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN A 747 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N MET A 776 " --> pdb=" O GLN A 747 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N CYS A 749 " --> pdb=" O MET A 776 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 840 through 844 removed outlier: 6.540A pdb=" N ARG A 816 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 843 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 818 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 817 " --> pdb=" O ASP A 868 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER A 898 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TRP A 871 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG A 900 " --> pdb=" O TRP A 871 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 168 through 171 Processing sheet with id= G, first strand: chain 'B' and resid 253 through 258 removed outlier: 6.892A pdb=" N VAL B 384 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N HIS B 355 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 386 " --> pdb=" O HIS B 355 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL B 448 " --> pdb=" O ARG B 385 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 387 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE B 450 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN B 389 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 452 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 301 through 306 Processing sheet with id= I, first strand: chain 'B' and resid 611 through 613 removed outlier: 6.242A pdb=" N LEU B 679 " --> pdb=" O ARG B 612 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 715 " --> pdb=" O TRP B 682 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 773 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU B 718 " --> pdb=" O LEU B 773 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 775 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLN B 747 " --> pdb=" O VAL B 774 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N MET B 776 " --> pdb=" O GLN B 747 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N CYS B 749 " --> pdb=" O MET B 776 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 840 through 844 removed outlier: 6.541A pdb=" N ARG B 816 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL B 843 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL B 818 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL B 817 " --> pdb=" O ASP B 868 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B 898 " --> pdb=" O PHE B 869 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TRP B 871 " --> pdb=" O SER B 898 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG B 900 " --> pdb=" O TRP B 871 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1098 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: 4.15 Time building geometry restraints manager: 6.39 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: 4485 1.34 - 1.46: 2920 1.46 - 1.58: 6201 1.58 - 1.70: 2 1.70 - 1.82: 114 Bond restraints: 13722 Sorted by residual: bond pdb=" C3 OAA A1002 " pdb=" O3 OAA A1002 " ideal model delta sigma weight residual 1.214 1.305 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C3 OAA B1001 " pdb=" O3 OAA B1001 " ideal model delta sigma weight residual 1.214 1.304 -0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C4 OAA B1001 " pdb=" O4 OAA B1001 " ideal model delta sigma weight residual 1.241 1.305 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C4 OAA A1002 " pdb=" O4 OAA A1002 " ideal model delta sigma weight residual 1.241 1.305 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" CA TRP B 871 " pdb=" CB TRP B 871 " ideal model delta sigma weight residual 1.527 1.451 0.076 2.48e-02 1.63e+03 9.47e+00 ... (remaining 13717 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.35: 323 105.35 - 113.21: 7355 113.21 - 121.06: 7031 121.06 - 128.91: 3732 128.91 - 136.76: 137 Bond angle restraints: 18578 Sorted by residual: angle pdb=" CA SER B 373 " pdb=" C SER B 373 " pdb=" N LYS B 374 " ideal model delta sigma weight residual 116.84 125.79 -8.95 1.71e+00 3.42e-01 2.74e+01 angle pdb=" CA SER A 373 " pdb=" C SER A 373 " pdb=" N LYS A 374 " ideal model delta sigma weight residual 116.84 125.78 -8.94 1.71e+00 3.42e-01 2.74e+01 angle pdb=" C GLY A 393 " pdb=" N PHE A 394 " pdb=" CA PHE A 394 " ideal model delta sigma weight residual 121.54 130.96 -9.42 1.91e+00 2.74e-01 2.43e+01 angle pdb=" N GLY B 142 " pdb=" CA GLY B 142 " pdb=" C GLY B 142 " ideal model delta sigma weight residual 113.18 102.21 10.97 2.37e+00 1.78e-01 2.14e+01 angle pdb=" CA TYR A 883 " pdb=" CB TYR A 883 " pdb=" CG TYR A 883 " ideal model delta sigma weight residual 113.90 105.78 8.12 1.80e+00 3.09e-01 2.03e+01 ... (remaining 18573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.90: 8015 25.90 - 51.79: 193 51.79 - 77.69: 14 77.69 - 103.58: 0 103.58 - 129.48: 2 Dihedral angle restraints: 8224 sinusoidal: 3362 harmonic: 4862 Sorted by residual: dihedral pdb=" CA GLU A 728 " pdb=" C GLU A 728 " pdb=" N HIS A 729 " pdb=" CA HIS A 729 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU B 728 " pdb=" C GLU B 728 " pdb=" N HIS B 729 " pdb=" CA HIS B 729 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA TYR A 883 " pdb=" C TYR A 883 " pdb=" N CYS A 884 " pdb=" CA CYS A 884 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1527 0.075 - 0.150: 410 0.150 - 0.225: 48 0.225 - 0.300: 3 0.300 - 0.375: 2 Chirality restraints: 1990 Sorted by residual: chirality pdb=" CB ILE A 609 " pdb=" CA ILE A 609 " pdb=" CG1 ILE A 609 " pdb=" CG2 ILE A 609 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE B 609 " pdb=" CA ILE B 609 " pdb=" CG1 ILE B 609 " pdb=" CG2 ILE B 609 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ASN A 140 " pdb=" N ASN A 140 " pdb=" C ASN A 140 " pdb=" CB ASN A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1987 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 829 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C LEU A 829 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 829 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 830 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 829 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C LEU B 829 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU B 829 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 830 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 398 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 399 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " 0.037 5.00e-02 4.00e+02 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 111 2.47 - 3.08: 8877 3.08 - 3.69: 21860 3.69 - 4.29: 30690 4.29 - 4.90: 49290 Nonbonded interactions: 110828 Sorted by model distance: nonbonded pdb=" OE1 GLU B 368 " pdb=" OG SER B 660 " model vdw 1.866 2.440 nonbonded pdb=" O LEU B 740 " pdb=" OH TYR B 849 " model vdw 2.197 2.440 nonbonded pdb=" O LEU A 740 " pdb=" OH TYR A 849 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR B 164 " pdb=" OE1 GLU B 189 " model vdw 2.256 2.440 nonbonded pdb=" OG SER B 909 " pdb=" O ALA B 911 " model vdw 2.264 2.440 ... (remaining 110823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 84 through 933) selection = (chain 'B' and resid 84 through 933) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 C 8434 2.51 5 N 2400 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.040 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.110 Process input model: 37.590 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.009 0.091 13722 Z= 0.605 Angle : 1.185 10.973 18578 Z= 0.639 Chirality : 0.066 0.375 1990 Planarity : 0.008 0.066 2454 Dihedral : 11.761 129.480 5100 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.39 % Favored : 89.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.16), residues: 1684 helix: -2.88 (0.15), residues: 654 sheet: -2.70 (0.32), residues: 190 loop : -3.12 (0.17), residues: 840 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.730 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2327 time to fit residues: 85.5121 Evaluate side-chains 141 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 185 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS A 390 ASN A 627 HIS A 631 HIS A 694 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 185 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS B 390 ASN B 627 HIS B 631 HIS B 694 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 13722 Z= 0.298 Angle : 0.733 8.303 18578 Z= 0.374 Chirality : 0.047 0.205 1990 Planarity : 0.006 0.054 2454 Dihedral : 7.927 118.670 1864 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.18), residues: 1684 helix: -1.48 (0.19), residues: 648 sheet: -2.70 (0.30), residues: 216 loop : -2.67 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.648 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.2077 time to fit residues: 65.1470 Evaluate side-chains 149 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13722 Z= 0.283 Angle : 0.697 6.790 18578 Z= 0.351 Chirality : 0.046 0.154 1990 Planarity : 0.005 0.045 2454 Dihedral : 7.585 116.403 1864 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.19), residues: 1684 helix: -1.01 (0.19), residues: 662 sheet: -2.74 (0.30), residues: 216 loop : -2.47 (0.21), residues: 806 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.655 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2296 time to fit residues: 70.0217 Evaluate side-chains 150 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 0.0010 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 145 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 13722 Z= 0.160 Angle : 0.623 7.241 18578 Z= 0.309 Chirality : 0.043 0.137 1990 Planarity : 0.004 0.040 2454 Dihedral : 7.049 117.110 1864 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.19), residues: 1684 helix: -0.70 (0.20), residues: 656 sheet: -2.49 (0.30), residues: 220 loop : -2.32 (0.21), residues: 808 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2236 time to fit residues: 81.3034 Evaluate side-chains 157 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN B 248 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 13722 Z= 0.214 Angle : 0.642 7.052 18578 Z= 0.318 Chirality : 0.044 0.246 1990 Planarity : 0.004 0.042 2454 Dihedral : 7.018 116.976 1864 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1684 helix: -0.53 (0.20), residues: 654 sheet: -2.37 (0.30), residues: 220 loop : -2.26 (0.21), residues: 810 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.647 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2109 time to fit residues: 68.6995 Evaluate side-chains 153 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 69.218 > 50: distance: 57 - 131: 24.253 distance: 67 - 134: 32.010 distance: 70 - 152: 28.087 distance: 115 - 120: 24.174 distance: 120 - 121: 23.875 distance: 121 - 122: 24.422 distance: 121 - 124: 25.497 distance: 122 - 123: 24.270 distance: 122 - 131: 11.883 distance: 124 - 125: 11.434 distance: 125 - 126: 34.943 distance: 125 - 127: 17.027 distance: 126 - 128: 13.563 distance: 127 - 129: 27.626 distance: 128 - 130: 8.737 distance: 129 - 130: 14.340 distance: 131 - 132: 16.663 distance: 132 - 133: 33.457 distance: 132 - 135: 38.215 distance: 133 - 134: 19.100 distance: 133 - 138: 15.919 distance: 135 - 136: 23.842 distance: 135 - 137: 9.705 distance: 138 - 139: 14.155 distance: 139 - 140: 9.501 distance: 139 - 142: 24.232 distance: 140 - 141: 39.327 distance: 140 - 152: 48.414 distance: 142 - 143: 4.179 distance: 143 - 144: 21.870 distance: 143 - 145: 15.128 distance: 145 - 147: 5.510 distance: 145 - 148: 4.342 distance: 146 - 147: 3.647 distance: 148 - 150: 4.484 distance: 149 - 151: 4.605 distance: 150 - 151: 5.134 distance: 152 - 153: 23.022 distance: 153 - 154: 14.246 distance: 153 - 156: 49.105 distance: 154 - 158: 36.508 distance: 156 - 157: 16.440 distance: 158 - 159: 5.303 distance: 159 - 160: 3.894 distance: 159 - 162: 11.661 distance: 160 - 167: 34.474 distance: 162 - 163: 4.474 distance: 163 - 164: 14.567 distance: 164 - 165: 6.581 distance: 164 - 166: 11.620 distance: 167 - 168: 11.773 distance: 168 - 169: 20.100 distance: 168 - 171: 35.750 distance: 169 - 170: 38.017 distance: 169 - 176: 22.477 distance: 171 - 172: 48.593 distance: 172 - 173: 4.478 distance: 173 - 174: 37.895 distance: 173 - 175: 23.741 distance: 176 - 177: 17.025 distance: 177 - 178: 9.987 distance: 177 - 180: 30.943 distance: 178 - 179: 42.331 distance: 178 - 185: 38.363 distance: 180 - 181: 14.956 distance: 181 - 182: 28.912 distance: 182 - 183: 43.635 distance: 182 - 184: 15.457 distance: 185 - 186: 5.045 distance: 185 - 191: 43.703 distance: 186 - 187: 36.087 distance: 186 - 189: 27.887 distance: 187 - 188: 17.188 distance: 187 - 192: 21.672 distance: 190 - 191: 37.282 distance: 192 - 193: 23.298 distance: 193 - 194: 25.993 distance: 193 - 196: 9.909 distance: 194 - 195: 35.650 distance: 194 - 200: 34.546 distance: 196 - 197: 20.905 distance: 197 - 198: 34.351 distance: 197 - 199: 20.235 distance: 200 - 201: 17.052 distance: 201 - 202: 32.106 distance: 201 - 204: 38.372 distance: 202 - 203: 39.323 distance: 202 - 208: 24.564 distance: 204 - 205: 9.059 distance: 205 - 206: 34.258 distance: 205 - 207: 29.564