Starting phenix.real_space_refine on Sun Sep 29 03:39:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/09_2024/6vl6_21231.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/09_2024/6vl6_21231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/09_2024/6vl6_21231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/09_2024/6vl6_21231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/09_2024/6vl6_21231.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/09_2024/6vl6_21231.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 13788 2.51 5 N 3564 2.21 5 O 4116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21504 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Restraints were copied for chains: O, N, Q, P, S, R, U, T, W, V, X, C, E, D, G, F, I, H, K, J, M, L Time building chain proxies: 6.12, per 1000 atoms: 0.28 Number of scatterers: 21504 At special positions: 0 Unit cell: (162.15, 158.7, 156.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 4116 8.00 N 3564 7.00 C 13788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 2.5 seconds 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 40 through 55 Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 18 through 33 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 90 through 105 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 18 through 33 Processing helix chain 'N' and resid 36 through 50 Processing helix chain 'N' and resid 52 through 67 Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 86 through 99 Processing helix chain 'D' and resid 5 through 20 Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 40 through 55 Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 90 through 105 Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'O' and resid 3 through 16 Processing helix chain 'O' and resid 18 through 33 Processing helix chain 'O' and resid 36 through 50 Processing helix chain 'O' and resid 52 through 67 Processing helix chain 'O' and resid 70 through 84 Processing helix chain 'O' and resid 86 through 99 Processing helix chain 'E' and resid 5 through 20 Processing helix chain 'E' and resid 22 through 36 Processing helix chain 'E' and resid 40 through 55 Processing helix chain 'E' and resid 56 through 71 Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 90 through 105 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'P' and resid 3 through 16 Processing helix chain 'P' and resid 18 through 33 Processing helix chain 'P' and resid 36 through 50 Processing helix chain 'P' and resid 52 through 67 Processing helix chain 'P' and resid 70 through 84 Processing helix chain 'P' and resid 86 through 99 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 40 through 55 Processing helix chain 'F' and resid 56 through 71 Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 90 through 105 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'Q' and resid 3 through 16 Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 67 Processing helix chain 'Q' and resid 70 through 84 Processing helix chain 'Q' and resid 86 through 99 Processing helix chain 'G' and resid 5 through 20 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 40 through 55 Processing helix chain 'G' and resid 56 through 71 Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 90 through 105 Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'R' and resid 3 through 16 Processing helix chain 'R' and resid 18 through 33 Processing helix chain 'R' and resid 36 through 50 Processing helix chain 'R' and resid 52 through 67 Processing helix chain 'R' and resid 70 through 84 Processing helix chain 'R' and resid 86 through 99 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 22 through 36 Processing helix chain 'H' and resid 40 through 55 Processing helix chain 'H' and resid 56 through 71 Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 90 through 105 Processing helix chain 'H' and resid 108 through 122 Processing helix chain 'S' and resid 3 through 16 Processing helix chain 'S' and resid 18 through 33 Processing helix chain 'S' and resid 36 through 50 Processing helix chain 'S' and resid 52 through 67 Processing helix chain 'S' and resid 70 through 84 Processing helix chain 'S' and resid 86 through 99 Processing helix chain 'I' and resid 5 through 20 Processing helix chain 'I' and resid 22 through 36 Processing helix chain 'I' and resid 40 through 55 Processing helix chain 'I' and resid 56 through 71 Processing helix chain 'I' and resid 74 through 88 Processing helix chain 'I' and resid 90 through 105 Processing helix chain 'I' and resid 108 through 122 Processing helix chain 'T' and resid 3 through 16 Processing helix chain 'T' and resid 18 through 33 Processing helix chain 'T' and resid 36 through 50 Processing helix chain 'T' and resid 52 through 67 Processing helix chain 'T' and resid 70 through 84 Processing helix chain 'T' and resid 86 through 99 Processing helix chain 'J' and resid 5 through 20 Processing helix chain 'J' and resid 22 through 36 Processing helix chain 'J' and resid 40 through 55 Processing helix chain 'J' and resid 56 through 71 Processing helix chain 'J' and resid 74 through 88 Processing helix chain 'J' and resid 90 through 105 Processing helix chain 'J' and resid 108 through 122 Processing helix chain 'U' and resid 3 through 16 Processing helix chain 'U' and resid 18 through 33 Processing helix chain 'U' and resid 36 through 50 Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 70 through 84 Processing helix chain 'U' and resid 86 through 99 Processing helix chain 'K' and resid 5 through 20 Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 40 through 55 Processing helix chain 'K' and resid 56 through 71 Processing helix chain 'K' and resid 74 through 88 Processing helix chain 'K' and resid 90 through 105 Processing helix chain 'K' and resid 108 through 122 Processing helix chain 'V' and resid 3 through 16 Processing helix chain 'V' and resid 18 through 33 Processing helix chain 'V' and resid 36 through 50 Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 70 through 84 Processing helix chain 'V' and resid 86 through 99 Processing helix chain 'L' and resid 5 through 20 Processing helix chain 'L' and resid 22 through 36 Processing helix chain 'L' and resid 40 through 55 Processing helix chain 'L' and resid 56 through 71 Processing helix chain 'L' and resid 74 through 88 Processing helix chain 'L' and resid 90 through 105 Processing helix chain 'L' and resid 108 through 122 Processing helix chain 'W' and resid 3 through 16 Processing helix chain 'W' and resid 18 through 33 Processing helix chain 'W' and resid 36 through 50 Processing helix chain 'W' and resid 52 through 67 Processing helix chain 'W' and resid 70 through 84 Processing helix chain 'W' and resid 86 through 99 Processing helix chain 'M' and resid 5 through 20 Processing helix chain 'M' and resid 22 through 36 Processing helix chain 'M' and resid 40 through 55 Processing helix chain 'M' and resid 56 through 71 Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 108 through 122 Processing helix chain 'X' and resid 3 through 16 Processing helix chain 'X' and resid 18 through 33 Processing helix chain 'X' and resid 36 through 50 Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 70 through 84 Processing helix chain 'X' and resid 86 through 99 1764 hydrogen bonds defined for protein. 5292 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: 6.66 Time building geometry restraints manager: 6.60 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: 4212 1.32 - 1.44: 6379 1.44 - 1.56: 11225 1.56 - 1.68: 84 1.68 - 1.81: 72 Bond restraints: 21972 Sorted by residual: bond pdb=" NE1 TRP O 40 " pdb=" CE2 TRP O 40 " ideal model delta sigma weight residual 1.370 1.326 0.044 1.10e-02 8.26e+03 1.58e+01 bond pdb=" NE1 TRP U 40 " pdb=" CE2 TRP U 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP Q 40 " pdb=" CE2 TRP Q 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP N 40 " pdb=" CE2 TRP N 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP B 40 " pdb=" CE2 TRP B 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.55e+01 ... (remaining 21967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 23496 1.64 - 3.27: 5137 3.27 - 4.91: 888 4.91 - 6.55: 155 6.55 - 8.18: 48 Bond angle restraints: 29724 Sorted by residual: angle pdb=" C ASP S 33 " pdb=" N PRO S 34 " pdb=" CA PRO S 34 " ideal model delta sigma weight residual 119.82 128.00 -8.18 9.80e-01 1.04e+00 6.97e+01 angle pdb=" C ASP T 33 " pdb=" N PRO T 34 " pdb=" CA PRO T 34 " ideal model delta sigma weight residual 119.82 128.00 -8.18 9.80e-01 1.04e+00 6.96e+01 angle pdb=" C ASP N 33 " pdb=" N PRO N 34 " pdb=" CA PRO N 34 " ideal model delta sigma weight residual 119.82 127.99 -8.17 9.80e-01 1.04e+00 6.95e+01 angle pdb=" C ASP R 33 " pdb=" N PRO R 34 " pdb=" CA PRO R 34 " ideal model delta sigma weight residual 119.82 127.99 -8.17 9.80e-01 1.04e+00 6.95e+01 angle pdb=" C ASP W 33 " pdb=" N PRO W 34 " pdb=" CA PRO W 34 " ideal model delta sigma weight residual 119.82 127.98 -8.16 9.80e-01 1.04e+00 6.93e+01 ... (remaining 29719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 12386 17.11 - 34.22: 539 34.22 - 51.33: 107 51.33 - 68.43: 48 68.43 - 85.54: 12 Dihedral angle restraints: 13092 sinusoidal: 5196 harmonic: 7896 Sorted by residual: dihedral pdb=" CB MET L 17 " pdb=" CG MET L 17 " pdb=" SD MET L 17 " pdb=" CE MET L 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.36 -39.36 3 1.50e+01 4.44e-03 6.97e+00 dihedral pdb=" CB MET F 17 " pdb=" CG MET F 17 " pdb=" SD MET F 17 " pdb=" CE MET F 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.35 -39.35 3 1.50e+01 4.44e-03 6.97e+00 dihedral pdb=" CB MET J 17 " pdb=" CG MET J 17 " pdb=" SD MET J 17 " pdb=" CE MET J 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.35 -39.35 3 1.50e+01 4.44e-03 6.97e+00 ... (remaining 13089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1719 0.065 - 0.130: 773 0.130 - 0.195: 398 0.195 - 0.260: 49 0.260 - 0.325: 25 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CA ASN E 80 " pdb=" N ASN E 80 " pdb=" C ASN E 80 " pdb=" CB ASN E 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ASN J 80 " pdb=" N ASN J 80 " pdb=" C ASN J 80 " pdb=" CB ASN J 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ASN K 80 " pdb=" N ASN K 80 " pdb=" C ASN K 80 " pdb=" CB ASN K 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2961 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR V 59 " -0.044 2.00e-02 2.50e+03 2.22e-02 9.84e+00 pdb=" CG TYR V 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR V 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR V 59 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR V 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR V 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR V 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR V 59 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 59 " 0.044 2.00e-02 2.50e+03 2.21e-02 9.75e+00 pdb=" CG TYR R 59 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR R 59 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR R 59 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR R 59 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR R 59 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR R 59 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR R 59 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 59 " -0.044 2.00e-02 2.50e+03 2.21e-02 9.73e+00 pdb=" CG TYR T 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR T 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR T 59 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR T 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR T 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR T 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR T 59 " -0.024 2.00e-02 2.50e+03 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 10121 2.92 - 3.42: 23687 3.42 - 3.91: 39439 3.91 - 4.41: 49797 4.41 - 4.90: 71062 Nonbonded interactions: 194106 Sorted by model distance: nonbonded pdb=" NZ LYS D 99 " pdb=" OD2 ASP O 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS C 99 " pdb=" OD2 ASP N 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS L 99 " pdb=" OD2 ASP W 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS A 99 " pdb=" OD2 ASP B 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS H 99 " pdb=" OD2 ASP S 88 " model vdw 2.431 3.120 ... (remaining 194101 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 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 39.340 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.019 0.086 21972 Z= 1.185 Angle : 1.456 8.182 29724 Z= 1.015 Chirality : 0.089 0.325 2964 Planarity : 0.008 0.041 3888 Dihedral : 11.376 85.543 8148 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 0.45 (0.14), residues: 2592 helix: 0.53 (0.09), residues: 2412 sheet: None (None), residues: 0 loop : -1.42 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP B 40 TYR 0.044 0.008 TYR V 59 ARG 0.006 0.001 ARG R 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 10 MET cc_start: 0.9149 (mmt) cc_final: 0.8679 (mtm) REVERT: A 32 LEU cc_start: 0.9706 (mt) cc_final: 0.9105 (tp) REVERT: A 108 ASN cc_start: 0.9462 (t0) cc_final: 0.8999 (t0) REVERT: A 110 ASP cc_start: 0.9268 (m-30) cc_final: 0.8932 (p0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2264 time to fit residues: 9.0785 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.114 Evaluate side-chains 31 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8664 (mt-10) REVERT: B 33 ASP cc_start: 0.9175 (t0) cc_final: 0.8910 (t0) REVERT: B 36 ASN cc_start: 0.9184 (t0) cc_final: 0.8950 (t0) REVERT: B 67 ASP cc_start: 0.9240 (t0) cc_final: 0.9023 (t0) REVERT: B 86 LYS cc_start: 0.9005 (mptt) cc_final: 0.8735 (mmtt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.3339 time to fit residues: 10.7592 Evaluate side-chains 17 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 197 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 0.0370 chunk 147 optimal weight: 8.9990 chunk 228 optimal weight: 0.1980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21972 Z= 0.213 Angle : 0.601 5.191 29724 Z= 0.324 Chirality : 0.041 0.147 2964 Planarity : 0.005 0.033 3888 Dihedral : 3.857 12.343 3072 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.60 % Allowed : 2.38 % Favored : 97.02 % 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: 1.33 (0.14), residues: 2592 helix: 1.11 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -1.85 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP U 74 TYR 0.016 0.002 TYR C 64 ARG 0.005 0.000 ARG X 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4934 Ramachandran restraints generated. 2467 Oldfield, 0 Emsley, 2467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4934 Ramachandran restraints generated. 2467 Oldfield, 0 Emsley, 2467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.120 Fit side-chains REVERT: I 32 LEU cc_start: 0.9794 (mt) cc_final: 0.9448 (mt) REVERT: I 108 ASN cc_start: 0.9312 (t0) cc_final: 0.8293 (t0) REVERT: I 110 ASP cc_start: 0.8359 (m-30) cc_final: 0.8068 (p0) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.1388 time to fit residues: 4.9019 Evaluate side-chains 21 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.106 Evaluate side-chains 25 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 11 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8774 (mm-30) REVERT: Q 33 ASP cc_start: 0.9422 (t0) cc_final: 0.8999 (t0) REVERT: Q 36 ASN cc_start: 0.9132 (t0) cc_final: 0.8360 (t0) REVERT: Q 67 ASP cc_start: 0.9335 (t0) cc_final: 0.9102 (t0) REVERT: Q 70 ASN cc_start: 0.9221 (t0) cc_final: 0.8672 (t0) REVERT: Q 86 LYS cc_start: 0.9130 (mptt) cc_final: 0.8783 (mmtt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2325 time to fit residues: 6.1156 Evaluate side-chains 16 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 0.0040 chunk 155 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 78 optimal weight: 0.0000 chunk 183 optimal weight: 0.0000 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21972 Z= 0.197 Angle : 0.775 18.201 29724 Z= 0.355 Chirality : 0.046 0.322 2964 Planarity : 0.004 0.030 3888 Dihedral : 3.954 13.742 3072 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: 0.92 (0.15), residues: 2592 helix: 0.87 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.37 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP U 74 TYR 0.029 0.002 TYR I 57 ARG 0.003 0.001 ARG M 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: I 10 MET cc_start: 0.8930 (mtm) cc_final: 0.7964 (mtm) REVERT: I 34 LEU cc_start: 0.9136 (mt) cc_final: 0.8882 (mt) REVERT: I 37 ASP cc_start: 0.9282 (t70) cc_final: 0.9076 (t0) REVERT: I 58 ASP cc_start: 0.9425 (p0) cc_final: 0.8967 (p0) REVERT: I 68 LEU cc_start: 0.9675 (pp) cc_final: 0.9395 (mt) REVERT: I 70 LEU cc_start: 0.9394 (mt) cc_final: 0.9159 (tt) REVERT: I 92 ASP cc_start: 0.8956 (p0) cc_final: 0.8726 (p0) REVERT: I 108 ASN cc_start: 0.9320 (t0) cc_final: 0.8391 (t0) REVERT: I 110 ASP cc_start: 0.8667 (m-30) cc_final: 0.8324 (p0) REVERT: I 113 GLU cc_start: 0.9118 (tt0) cc_final: 0.8859 (tm-30) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1083 time to fit residues: 3.8014 Evaluate side-chains 16 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.111 Evaluate side-chains 26 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8778 (mm-30) REVERT: N 33 ASP cc_start: 0.9390 (t0) cc_final: 0.9071 (t0) REVERT: N 36 ASN cc_start: 0.9046 (t0) cc_final: 0.8323 (t0) REVERT: N 38 GLU cc_start: 0.8300 (pm20) cc_final: 0.8033 (pm20) REVERT: N 70 ASN cc_start: 0.9224 (t0) cc_final: 0.8464 (t0) REVERT: N 86 LYS cc_start: 0.9031 (mptt) cc_final: 0.8802 (mmtp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.2379 time to fit residues: 6.5214 Evaluate side-chains 16 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 4.9990 chunk 172 optimal weight: 0.3980 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 153 optimal weight: 0.0870 chunk 230 optimal weight: 0.4980 chunk 243 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 218 optimal weight: 0.0060 chunk 65 optimal weight: 2.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21972 Z= 0.320 Angle : 0.941 18.157 29724 Z= 0.414 Chirality : 0.044 0.172 2964 Planarity : 0.004 0.030 3888 Dihedral : 4.083 13.461 3072 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 0.40 (0.15), residues: 2592 helix: 0.55 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.74 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 74 TYR 0.011 0.002 TYR A 64 ARG 0.007 0.001 ARG U 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.106 Fit side-chains REVERT: D 34 LEU cc_start: 0.9045 (mt) cc_final: 0.8798 (mt) REVERT: D 37 ASP cc_start: 0.9312 (t70) cc_final: 0.9076 (t0) REVERT: D 68 LEU cc_start: 0.9631 (pp) cc_final: 0.9377 (mt) REVERT: D 70 LEU cc_start: 0.9311 (mt) cc_final: 0.9099 (tt) REVERT: D 108 ASN cc_start: 0.9287 (t0) cc_final: 0.8472 (t0) REVERT: D 110 ASP cc_start: 0.8763 (m-30) cc_final: 0.8374 (p0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0699 time to fit residues: 2.2160 Evaluate side-chains 13 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.106 Evaluate side-chains 22 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: Q 33 ASP cc_start: 0.9493 (t0) cc_final: 0.9080 (t0) REVERT: Q 36 ASN cc_start: 0.9208 (t0) cc_final: 0.8412 (t0) REVERT: Q 70 ASN cc_start: 0.9077 (t0) cc_final: 0.8220 (t0) REVERT: Q 86 LYS cc_start: 0.9145 (mptt) cc_final: 0.8841 (mmtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2202 time to fit residues: 5.1520 Evaluate side-chains 17 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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: 61.4192 > 50: distance: 0 - 1: 5.432 distance: 1 - 2: 16.438 distance: 1 - 4: 16.641 distance: 2 - 3: 5.966 distance: 2 - 12: 18.491 distance: 3 - 32: 16.056 distance: 4 - 5: 33.797 distance: 5 - 6: 29.688 distance: 5 - 7: 34.673 distance: 6 - 8: 22.422 distance: 7 - 9: 10.370 distance: 8 - 10: 38.245 distance: 9 - 10: 24.002 distance: 10 - 11: 24.016 distance: 12 - 13: 16.618 distance: 13 - 14: 5.646 distance: 13 - 16: 23.316 distance: 14 - 19: 35.532 distance: 15 - 40: 36.442 distance: 16 - 17: 17.469 distance: 16 - 18: 7.625 distance: 19 - 20: 16.077 distance: 20 - 21: 14.595 distance: 20 - 23: 11.177 distance: 21 - 22: 24.324 distance: 21 - 27: 21.198 distance: 22 - 48: 41.871 distance: 23 - 24: 11.519 distance: 24 - 25: 22.867 distance: 24 - 26: 12.986 distance: 27 - 28: 12.067 distance: 28 - 29: 15.765 distance: 28 - 31: 3.289 distance: 29 - 30: 27.960 distance: 29 - 32: 20.471 distance: 32 - 33: 14.771 distance: 33 - 34: 6.991 distance: 33 - 36: 19.759 distance: 34 - 35: 16.013 distance: 34 - 40: 9.724 distance: 36 - 37: 18.482 distance: 37 - 38: 39.709 distance: 37 - 39: 20.107 distance: 40 - 41: 14.220 distance: 41 - 42: 11.693 distance: 41 - 44: 3.969 distance: 42 - 43: 22.602 distance: 42 - 48: 24.237 distance: 44 - 45: 28.540 distance: 45 - 46: 45.015 distance: 45 - 47: 26.026 distance: 48 - 49: 12.458 distance: 49 - 50: 10.703 distance: 49 - 52: 31.493 distance: 50 - 51: 37.477 distance: 50 - 57: 26.781 distance: 52 - 53: 41.765 distance: 53 - 54: 36.249 distance: 54 - 55: 60.609 distance: 55 - 56: 43.531 distance: 57 - 58: 19.849 distance: 58 - 59: 10.368 distance: 58 - 61: 7.659 distance: 59 - 60: 33.937 distance: 59 - 65: 14.350 distance: 61 - 62: 18.216 distance: 62 - 63: 24.515 distance: 62 - 64: 24.548 distance: 65 - 66: 27.866 distance: 65 - 71: 13.596 distance: 66 - 67: 25.120 distance: 66 - 69: 23.926 distance: 67 - 68: 13.675 distance: 67 - 72: 19.781 distance: 69 - 70: 33.316 distance: 70 - 71: 28.074 distance: 72 - 73: 6.765 distance: 73 - 74: 6.017 distance: 73 - 76: 3.376 distance: 74 - 75: 13.541 distance: 76 - 77: 5.568 distance: 77 - 78: 9.716 distance: 77 - 79: 7.484