Starting phenix.real_space_refine on Sat Mar 16 04:38:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/03_2024/6nzo_0559.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/03_2024/6nzo_0559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/03_2024/6nzo_0559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/03_2024/6nzo_0559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/03_2024/6nzo_0559.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/03_2024/6nzo_0559.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 290 5.49 5 S 32 5.16 5 C 7707 2.51 5 N 2563 2.21 5 O 3143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13738 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 752 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "S" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1819 Unusual residues: {' ZN': 3} Classifications: {'peptide': 233, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 223, None: 3} Not linked: pdbres="THR S 325 " pdbres=" ZN S1001 " Not linked: pdbres=" ZN S1001 " pdbres=" ZN S1002 " Not linked: pdbres=" ZN S1002 " pdbres=" ZN S1003 " Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12284 SG CYS S 143 60.709 80.388 47.265 1.00109.22 S ATOM 12396 SG CYS S 158 59.164 84.192 47.848 1.00101.19 S ATOM 12429 SG CYS S 163 61.766 82.563 50.683 1.00113.64 S ATOM 12466 SG CYS S 169 61.843 82.802 46.265 1.00112.25 S ATOM 12173 SG CYS S 129 58.781 80.486 51.064 1.00112.66 S ATOM 12187 SG CYS S 131 58.804 77.494 49.481 1.00118.61 S ATOM 12284 SG CYS S 143 60.709 80.388 47.265 1.00109.22 S ATOM 12325 SG CYS S 149 58.199 78.606 47.178 1.00 92.28 S ATOM 13234 SG CYS S 261 37.901 89.429 19.020 1.00124.70 S ATOM 13613 SG CYS S 308 40.146 91.851 16.557 1.00133.16 S ATOM 13631 SG CYS S 310 40.500 89.796 15.425 1.00135.88 S ATOM 13665 SG CYS S 315 37.577 90.841 15.137 1.00131.95 S Time building chain proxies: 7.16, per 1000 atoms: 0.52 Number of scatterers: 13738 At special positions: 0 Unit cell: (83.2, 146.64, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 32 16.00 P 290 15.00 O 3143 8.00 N 2563 7.00 C 7707 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: 6.56 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 169 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 158 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 163 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 129 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 149 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 131 " pdb=" ZN S1003 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 308 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 315 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 310 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 261 " Number of angles added : 18 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 14 sheets defined 58.8% alpha, 5.8% beta 143 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 6.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.552A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.718A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.561A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.633A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.003A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.926A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.392A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.546A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 155 removed outlier: 3.601A pdb=" N LYS S 155 " --> pdb=" O ARG S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 230 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.607A pdb=" N ARG S 255 " --> pdb=" O ASN S 252 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE S 256 " --> pdb=" O LEU S 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 252 through 256' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.828A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.726A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.271A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'S' and resid 182 through 187 Processing sheet with id=AB4, first strand: chain 'S' and resid 205 through 208 removed outlier: 6.715A pdb=" N PHE S 205 " --> pdb=" O ALA S 282 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA S 282 " --> pdb=" O PHE S 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 212 through 214 443 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2233 1.33 - 1.45: 4991 1.45 - 1.57: 6723 1.57 - 1.69: 578 1.69 - 1.81: 46 Bond restraints: 14571 Sorted by residual: bond pdb=" C ASP S 134 " pdb=" N TRP S 135 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.23e-02 6.61e+03 2.32e+01 bond pdb=" C ILE G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.392 -0.058 1.51e-02 4.39e+03 1.45e+01 bond pdb=" C3' DC I 143 " pdb=" O3' DC I 143 " ideal model delta sigma weight residual 1.422 1.500 -0.078 3.00e-02 1.11e+03 6.72e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.95e+00 bond pdb=" C ILE E 51 " pdb=" N ARG E 52 " ideal model delta sigma weight residual 1.335 1.366 -0.032 1.36e-02 5.41e+03 5.42e+00 ... (remaining 14566 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.48: 1460 105.48 - 112.92: 7993 112.92 - 120.36: 6086 120.36 - 127.81: 4928 127.81 - 135.25: 442 Bond angle restraints: 20909 Sorted by residual: angle pdb=" N PRO S 88 " pdb=" CA PRO S 88 " pdb=" CB PRO S 88 " ideal model delta sigma weight residual 103.00 110.43 -7.43 1.10e+00 8.26e-01 4.56e+01 angle pdb=" N PRO S 89 " pdb=" CA PRO S 89 " pdb=" CB PRO S 89 " ideal model delta sigma weight residual 103.38 110.40 -7.02 1.05e+00 9.07e-01 4.47e+01 angle pdb=" N PRO S 84 " pdb=" CA PRO S 84 " pdb=" CB PRO S 84 " ideal model delta sigma weight residual 103.00 110.24 -7.24 1.10e+00 8.26e-01 4.33e+01 angle pdb=" C SER S 122 " pdb=" N ASP S 123 " pdb=" CA ASP S 123 " ideal model delta sigma weight residual 122.61 129.82 -7.21 1.56e+00 4.11e-01 2.14e+01 angle pdb=" N VAL S 159 " pdb=" CA VAL S 159 " pdb=" C VAL S 159 " ideal model delta sigma weight residual 110.05 105.60 4.45 1.09e+00 8.42e-01 1.67e+01 ... (remaining 20904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 6484 34.58 - 69.17: 1505 69.17 - 103.75: 15 103.75 - 138.33: 0 138.33 - 172.91: 4 Dihedral angle restraints: 8008 sinusoidal: 5161 harmonic: 2847 Sorted by residual: dihedral pdb=" CA GLN S 172 " pdb=" C GLN S 172 " pdb=" N ARG S 173 " pdb=" CA ARG S 173 " ideal model delta harmonic sigma weight residual 180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA GLU S 133 " pdb=" C GLU S 133 " pdb=" N ASP S 134 " pdb=" CA ASP S 134 " ideal model delta harmonic sigma weight residual 180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 47.09 172.91 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1700 0.056 - 0.112: 531 0.112 - 0.168: 91 0.168 - 0.224: 23 0.224 - 0.280: 6 Chirality restraints: 2351 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA GLU S 216 " pdb=" N GLU S 216 " pdb=" C GLU S 216 " pdb=" CB GLU S 216 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2348 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 102 " -0.038 2.00e-02 2.50e+03 1.77e-02 9.39e+00 pdb=" N9 DG I 102 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 102 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DG I 102 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 102 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG I 102 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 102 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 102 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 102 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG I 102 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 102 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.040 2.00e-02 2.50e+03 1.78e-02 8.71e+00 pdb=" N9 DA I 20 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 106 " 0.037 2.00e-02 2.50e+03 1.61e-02 7.82e+00 pdb=" N9 DG J 106 " -0.038 2.00e-02 2.50e+03 pdb=" C8 DG J 106 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG J 106 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 106 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG J 106 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 106 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DG J 106 " -0.010 2.00e-02 2.50e+03 pdb=" N2 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 106 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 106 " -0.004 2.00e-02 2.50e+03 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3615 2.83 - 3.35: 11979 3.35 - 3.87: 27098 3.87 - 4.38: 30302 4.38 - 4.90: 43766 Nonbonded interactions: 116760 Sorted by model distance: nonbonded pdb=" O CYS S 129 " pdb=" ND2 ASN S 164 " model vdw 2.313 2.520 nonbonded pdb=" O SER D 120 " pdb=" OG SER D 120 " model vdw 2.322 2.440 nonbonded pdb=" O SER S 260 " pdb=" ND2 ASN S 295 " model vdw 2.333 2.520 nonbonded pdb=" CB THR H 29 " pdb=" OP1 DT I 104 " model vdw 2.333 3.470 nonbonded pdb=" O LYS S 190 " pdb=" ND2 ASN S 258 " model vdw 2.352 2.520 ... (remaining 116755 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' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = (chain 'F' and resid 24 through 100) } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = (chain 'G' and (resid 16 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = (chain 'D' and resid 26 through 120) selection = chain 'H' } 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=0.89 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: 0.770 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: 3.710 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 43.570 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.007 0.078 14571 Z= 0.401 Angle : 0.926 10.246 20909 Z= 0.563 Chirality : 0.056 0.280 2351 Planarity : 0.007 0.056 1659 Dihedral : 27.022 172.914 6176 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.00 % 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: -1.08 (0.24), residues: 961 helix: 0.15 (0.19), residues: 551 sheet: -2.07 (0.76), residues: 45 loop : -1.82 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 135 HIS 0.003 0.001 HIS G 31 PHE 0.024 0.003 PHE B 61 TYR 0.016 0.003 TYR H 118 ARG 0.007 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 TYR cc_start: 0.7762 (m-80) cc_final: 0.7551 (m-10) REVERT: G 102 ILE cc_start: 0.9044 (mt) cc_final: 0.8705 (mm) REVERT: H 27 ARG cc_start: 0.7646 (mmm160) cc_final: 0.6481 (ptp-170) REVERT: H 37 TYR cc_start: 0.8260 (m-80) cc_final: 0.8017 (m-80) REVERT: H 42 LEU cc_start: 0.8182 (tp) cc_final: 0.7827 (tp) REVERT: H 56 MET cc_start: 0.7288 (tpp) cc_final: 0.7018 (mmp) REVERT: H 68 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6901 (tm-30) REVERT: S 201 GLN cc_start: 0.8295 (tt0) cc_final: 0.7894 (tp40) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.3702 time to fit residues: 124.5214 Evaluate side-chains 165 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS E 68 GLN E 85 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 38 ASN ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 215 ASN S 242 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14571 Z= 0.227 Angle : 0.605 7.326 20909 Z= 0.358 Chirality : 0.036 0.162 2351 Planarity : 0.005 0.059 1659 Dihedral : 30.023 171.940 4260 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.18 % Allowed : 12.73 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 961 helix: 1.79 (0.21), residues: 556 sheet: -1.72 (0.82), residues: 45 loop : -1.34 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 135 HIS 0.007 0.001 HIS F 75 PHE 0.011 0.002 PHE H 67 TYR 0.016 0.002 TYR G 39 ARG 0.010 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8489 (tp-100) REVERT: A 79 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8328 (ttmt) REVERT: B 25 ASN cc_start: 0.8008 (p0) cc_final: 0.7781 (p0) REVERT: B 30 THR cc_start: 0.8145 (p) cc_final: 0.7804 (t) REVERT: G 102 ILE cc_start: 0.9008 (mt) cc_final: 0.8738 (mm) REVERT: G 104 GLN cc_start: 0.8493 (mp10) cc_final: 0.8162 (mp10) REVERT: H 27 ARG cc_start: 0.7781 (mmm160) cc_final: 0.6549 (ptp-170) REVERT: H 28 LYS cc_start: 0.7412 (tttm) cc_final: 0.7158 (mmtt) REVERT: H 37 TYR cc_start: 0.8146 (m-80) cc_final: 0.7719 (m-80) REVERT: H 68 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7157 (tm-30) REVERT: H 79 HIS cc_start: 0.7890 (t70) cc_final: 0.7514 (t70) REVERT: S 154 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8206 (m) REVERT: S 185 ILE cc_start: 0.6072 (tp) cc_final: 0.5831 (tp) REVERT: S 227 ASP cc_start: 0.6286 (m-30) cc_final: 0.6072 (p0) REVERT: S 244 PHE cc_start: 0.5742 (m-80) cc_final: 0.5080 (m-80) outliers start: 26 outliers final: 16 residues processed: 218 average time/residue: 0.2932 time to fit residues: 88.1203 Evaluate side-chains 196 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 223 MET Chi-restraints excluded: chain S residue 256 PHE Chi-restraints excluded: chain S residue 265 CYS Chi-restraints excluded: chain S residue 272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 110 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS B 27 GLN B 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 14571 Z= 0.458 Angle : 0.773 7.417 20909 Z= 0.441 Chirality : 0.044 0.198 2351 Planarity : 0.006 0.062 1659 Dihedral : 30.545 178.582 4260 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.39 % Allowed : 15.67 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 961 helix: 1.15 (0.21), residues: 553 sheet: -1.85 (0.82), residues: 45 loop : -1.52 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP S 135 HIS 0.007 0.002 HIS S 141 PHE 0.023 0.003 PHE C 25 TYR 0.025 0.003 TYR D 80 ARG 0.006 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 194 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8708 (tp-100) REVERT: C 38 ASN cc_start: 0.7697 (t0) cc_final: 0.7427 (m-40) REVERT: E 109 LEU cc_start: 0.8064 (tt) cc_final: 0.7810 (tt) REVERT: F 100 PHE cc_start: 0.8092 (m-80) cc_final: 0.7548 (m-10) REVERT: G 102 ILE cc_start: 0.9102 (mt) cc_final: 0.8852 (mm) REVERT: H 27 ARG cc_start: 0.8000 (mmm160) cc_final: 0.6715 (ptp-170) REVERT: H 68 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7446 (tm-30) REVERT: S 109 ILE cc_start: 0.4783 (pt) cc_final: 0.4260 (pt) REVERT: S 176 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7270 (ttp-110) REVERT: S 214 ILE cc_start: 0.5173 (OUTLIER) cc_final: 0.4931 (pt) REVERT: S 223 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8176 (ptp) REVERT: S 227 ASP cc_start: 0.6560 (m-30) cc_final: 0.6072 (p0) REVERT: S 278 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7176 (mtm) outliers start: 44 outliers final: 33 residues processed: 219 average time/residue: 0.2872 time to fit residues: 87.2727 Evaluate side-chains 210 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 223 MET Chi-restraints excluded: chain S residue 256 PHE Chi-restraints excluded: chain S residue 265 CYS Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 278 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 54.4321 > 50: distance: 25 - 27: 3.102 distance: 27 - 28: 7.088 distance: 28 - 31: 3.242 distance: 29 - 30: 5.507 distance: 29 - 36: 5.232 distance: 30 - 181: 8.681 distance: 31 - 32: 7.244 distance: 32 - 33: 4.149 distance: 33 - 35: 7.168 distance: 36 - 37: 6.802 distance: 37 - 38: 10.634 distance: 37 - 40: 8.549 distance: 38 - 39: 18.845 distance: 38 - 43: 10.548 distance: 40 - 41: 9.697 distance: 40 - 42: 4.858 distance: 43 - 44: 7.275 distance: 43 - 167: 14.456 distance: 44 - 45: 15.684 distance: 44 - 47: 14.504 distance: 45 - 46: 6.735 distance: 45 - 51: 13.164 distance: 46 - 164: 6.534 distance: 47 - 48: 12.036 distance: 47 - 49: 17.046 distance: 48 - 50: 9.719 distance: 51 - 52: 8.174 distance: 52 - 53: 10.991 distance: 52 - 55: 11.588 distance: 53 - 54: 6.217 distance: 53 - 59: 11.872 distance: 54 - 82: 22.919 distance: 55 - 56: 12.325 distance: 56 - 57: 8.362 distance: 56 - 58: 17.176 distance: 59 - 60: 7.471 distance: 60 - 61: 11.766 distance: 60 - 63: 14.680 distance: 61 - 62: 7.800 distance: 61 - 68: 8.643 distance: 62 - 93: 12.746 distance: 63 - 64: 22.119 distance: 64 - 65: 7.348 distance: 65 - 66: 15.595 distance: 65 - 67: 8.586 distance: 68 - 69: 9.181 distance: 68 - 74: 12.230 distance: 69 - 70: 15.691 distance: 69 - 72: 15.167 distance: 70 - 71: 9.111 distance: 70 - 75: 7.247 distance: 71 - 104: 17.760 distance: 72 - 73: 20.121 distance: 73 - 74: 6.587 distance: 75 - 76: 4.384 distance: 76 - 77: 8.689 distance: 76 - 79: 14.736 distance: 77 - 78: 9.200 distance: 78 - 110: 12.438 distance: 79 - 80: 21.040 distance: 79 - 81: 36.015 distance: 83 - 84: 7.449 distance: 83 - 86: 13.859 distance: 84 - 85: 9.766 distance: 84 - 93: 6.023 distance: 85 - 121: 10.614 distance: 86 - 87: 9.169 distance: 87 - 88: 9.134 distance: 87 - 89: 7.058 distance: 88 - 90: 9.210 distance: 89 - 91: 6.190 distance: 90 - 92: 10.330 distance: 91 - 92: 5.013 distance: 93 - 94: 4.092 distance: 94 - 95: 5.658 distance: 94 - 97: 5.854 distance: 95 - 104: 4.968 distance: 96 - 129: 6.459 distance: 97 - 98: 8.373 distance: 98 - 99: 5.934 distance: 99 - 100: 10.761 distance: 100 - 101: 6.143 distance: 101 - 102: 7.352 distance: 101 - 103: 6.474 distance: 104 - 105: 5.486 distance: 105 - 106: 7.644 distance: 105 - 108: 4.784 distance: 106 - 107: 4.183 distance: 107 - 136: 3.466 distance: 108 - 109: 6.148