Starting phenix.real_space_refine on Fri Jan 19 15:31:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e49_27884/01_2024/8e49_27884_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e49_27884/01_2024/8e49_27884.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e49_27884/01_2024/8e49_27884_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e49_27884/01_2024/8e49_27884_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e49_27884/01_2024/8e49_27884_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e49_27884/01_2024/8e49_27884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e49_27884/01_2024/8e49_27884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e49_27884/01_2024/8e49_27884_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e49_27884/01_2024/8e49_27884_neut_trim_updated.pdb" } resolution = 2.05 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= -0.023 sd= 0.881 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: 7 Type Number sf(0) Gaussians P 3022 5.49 5 S 28 5.16 5 C 34614 2.51 5 N 13706 2.21 5 O 22615 1.98 5 F 1 1.80 5 H 41885 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 35": "OE1" <-> "OE2" Residue "K ASP 98": "OD1" <-> "OD2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 236": "OE1" <-> "OE2" Residue "K ASP 264": "OD1" <-> "OD2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ASP 141": "OD1" <-> "OD2" Residue "P ASP 34": "OD1" <-> "OD2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ASP 94": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 115871 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93491 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 278, 'rna2p_pyr': 152, 'rna3p': 15, 'rna3p_pur': 1387, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 436, 'rna3p': 2461} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 279, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1386, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 436, 'rna3p': 2461} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 100554 Chain: "J" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3810 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2182 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3170 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3182 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "O" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2291 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "P" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1775 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 898 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "R" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 794 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'UH0': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" P A G I2505 " occ=0.54 ... (66 atoms not shown) pdb=" H22B G I2505 " occ=0.46 residue: pdb=" P A U I2506 " occ=0.54 ... (58 atoms not shown) pdb=" H6 B U I2506 " occ=0.46 residue: pdb=" P A C I2507 " occ=0.54 ... (60 atoms not shown) pdb=" H6 B C I2507 " occ=0.46 residue: pdb=" P A C I2601 " occ=0.57 ... (60 atoms not shown) pdb=" H6 B C I2601 " occ=0.43 residue: pdb=" P A A I2602 " occ=0.57 ... (64 atoms not shown) pdb=" H2 B A I2602 " occ=0.43 residue: pdb=" P A G I2603 " occ=0.57 ... (66 atoms not shown) pdb=" H22B G I2603 " occ=0.43 Time building chain proxies: 66.48, per 1000 atoms: 0.57 Number of scatterers: 115871 At special positions: 0 Unit cell: (230.482, 223.047, 190.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 28 16.00 P 3022 15.00 F 1 9.00 O 22615 8.00 N 13706 7.00 C 34614 6.00 H 41885 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 79.11 Conformation dependent library (CDL) restraints added in 2.2 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 35 helices and 13 sheets defined 29.8% alpha, 14.8% beta 909 base pairs and 1594 stacking pairs defined. Time for finding SS restraints: 59.90 Creating SS restraints... Processing helix chain 'K' and resid 10 through 17 removed outlier: 3.563A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 17' Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.919A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 30 through 35' Processing helix chain 'K' and resid 131 through 136 removed outlier: 3.603A pdb=" N ILE K 135 " --> pdb=" O PRO K 131 " (cutoff:3.500A) Proline residue: K 136 - end of helix No H-bonds generated for 'chain 'K' and resid 131 through 136' Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.858A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.018A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.553A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 6.785A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.908A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.643A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 40 removed outlier: 3.753A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.503A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.615A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.531A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 removed outlier: 3.559A pdb=" N GLU M 197 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.727A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.562A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.504A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 98 through 103' Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'O' and resid 24 through 38 removed outlier: 3.708A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.169A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 122 removed outlier: 4.075A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.523A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.795A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 70 removed outlier: 3.669A pdb=" N LEU P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LYS P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 65 through 70' Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.854A pdb=" N HIS Q 19 " --> pdb=" O MET Q 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 16 Processing helix chain 'R' and resid 17 through 24 removed outlier: 4.240A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.619A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 162 through 165 removed outlier: 6.554A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.224A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'M' and resid 1 through 6 removed outlier: 3.561A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 44 through 47 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.723A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'N' and resid 11 through 16 removed outlier: 4.139A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER N 199 " --> pdb=" O LYS N 8 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU N 168 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 79 through 84 removed outlier: 5.964A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 179 through 182 removed outlier: 3.514A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 24 through 28 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'N' and resid 105 through 108 removed outlier: 5.716A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'O' and resid 14 through 19 Processing sheet with id= 13, first strand: chain 'P' and resid 2 through 8 247 hydrogen bonds defined for protein. 738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2265 hydrogen bonds 3550 hydrogen bond angles 0 basepair planarities 909 basepair parallelities 1597 stacking parallelities Total time for adding SS restraints: 156.19 Time building geometry restraints manager: 83.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 41883 1.03 - 1.23: 629 1.23 - 1.42: 43321 1.42 - 1.62: 37897 1.62 - 1.81: 54 Bond restraints: 123784 Sorted by residual: bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+02 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.413 0.389 2.00e-02 2.50e+03 3.79e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.369 0.266 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.349 -0.194 2.00e-02 2.50e+03 9.40e+01 ... (remaining 123779 not shown) Histogram of bond angle deviations from ideal: 75.01 - 86.98: 6 86.98 - 98.95: 0 98.95 - 110.91: 113364 110.91 - 122.88: 87518 122.88 - 134.85: 20805 Bond angle restraints: 221693 Sorted by residual: angle pdb=" O3' A I2062 " pdb=" C3' A I2062 " pdb=" H3' A I2062 " ideal model delta sigma weight residual 109.00 75.01 33.99 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C1' G7M I2069 " pdb=" N9 G7M I2069 " pdb=" C8 G7M I2069 " ideal model delta sigma weight residual 94.96 128.71 -33.75 3.00e+00 1.11e-01 1.27e+02 angle pdb=" N9 B A I2602 " pdb=" C1'B A I2602 " pdb=" H1'B A I2602 " ideal model delta sigma weight residual 109.00 75.68 33.32 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C18 UH0 I3001 " pdb=" C19 UH0 I3001 " pdb=" N5 UH0 I3001 " ideal model delta sigma weight residual 154.20 122.58 31.62 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C2'B A I2602 " pdb=" C1'B A I2602 " pdb=" H1'B A I2602 " ideal model delta sigma weight residual 109.00 78.76 30.24 3.00e+00 1.11e-01 1.02e+02 ... (remaining 221688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 52871 35.91 - 71.81: 5400 71.81 - 107.72: 795 107.72 - 143.62: 7 143.62 - 179.53: 6 Dihedral angle restraints: 59079 sinusoidal: 55429 harmonic: 3650 Sorted by residual: dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual -128.00 51.53 -179.53 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4'A U I2506 " pdb=" C1'A U I2506 " pdb=" N1 A U I2506 " pdb=" C2 A U I2506 " ideal model delta sinusoidal sigma weight residual 232.00 52.84 179.16 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4'B C I2601 " pdb=" C1'B C I2601 " pdb=" N1 B C I2601 " pdb=" C2 B C I2601 " ideal model delta sinusoidal sigma weight residual 232.00 61.06 170.94 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 59076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 16447 0.169 - 0.338: 1 0.338 - 0.507: 0 0.507 - 0.676: 0 0.676 - 0.845: 2 Chirality restraints: 16450 Sorted by residual: chirality pdb=" C3' A I2062 " pdb=" C4' A I2062 " pdb=" O3' A I2062 " pdb=" C2' A I2062 " both_signs ideal model delta sigma weight residual False -2.48 -1.63 -0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" C1'B A I2602 " pdb=" O4'B A I2602 " pdb=" C2'B A I2602 " pdb=" N9 B A I2602 " both_signs ideal model delta sigma weight residual False 2.44 1.60 0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" C3 UH0 I3001 " pdb=" C2 UH0 I3001 " pdb=" C4 UH0 I3001 " pdb=" N1 UH0 I3001 " both_signs ideal model delta sigma weight residual False 2.55 2.83 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 16447 not shown) Planarity restraints: 8169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.033 2.00e-02 2.50e+03 6.02e-01 8.15e+03 pdb=" C4' OMC I2498 " 0.461 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.755 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.589 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.585 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.224 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.894 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.202 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.045 2.00e-02 2.50e+03 5.78e-01 7.51e+03 pdb=" C4' 2MG I2445 " -0.436 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.627 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.588 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.200 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.925 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.228 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.877 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.027 2.00e-02 2.50e+03 5.70e-01 7.32e+03 pdb=" C4' 2MG I1835 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.651 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.554 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.216 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.893 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.228 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.871 2.00e-02 2.50e+03 ... (remaining 8166 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 2726 2.09 - 2.72: 130743 2.72 - 3.35: 284210 3.35 - 3.97: 445776 3.97 - 4.60: 637105 Nonbonded interactions: 1500560 Sorted by model distance: nonbonded pdb=" OE1 GLU M 198 " pdb=" H GLU M 198 " model vdw 1.466 1.850 nonbonded pdb=" OE1 GLU M 144 " pdb=" H GLU M 144 " model vdw 1.496 1.850 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.530 1.850 nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.568 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.571 1.850 ... (remaining 1500555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.900 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: 0.910 Extract box with map and model: 30.950 Check model and map are aligned: 1.300 Set scattering table: 0.800 Process input model: 465.960 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:9.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 519.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 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 : 0.005 0.390 81899 Z= 0.311 Angle : 0.415 33.754 125756 Z= 0.203 Chirality : 0.025 0.845 16450 Planarity : 0.022 0.602 4636 Dihedral : 22.347 179.527 48242 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.85 % Allowed : 15.50 % Favored : 83.65 % 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: 0.91 (0.25), residues: 1163 helix: 1.84 (0.34), residues: 250 sheet: 1.12 (0.40), residues: 182 loop : 0.09 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 248 HIS 0.003 0.001 HIS K 230 PHE 0.006 0.001 PHE K 240 TYR 0.005 0.001 TYR P 38 ARG 0.010 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 3.209 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 201 average time/residue: 2.9953 time to fit residues: 761.6384 Evaluate side-chains 197 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 190 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 40.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 ASN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 81899 Z= 0.348 Angle : 0.619 14.728 125756 Z= 0.341 Chirality : 0.040 0.886 16450 Planarity : 0.007 0.135 4636 Dihedral : 22.262 177.403 46010 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 1.70 % Allowed : 14.01 % Favored : 84.29 % 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: 0.58 (0.25), residues: 1163 helix: 1.44 (0.33), residues: 270 sheet: 0.90 (0.39), residues: 174 loop : -0.12 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.008 0.001 HIS K 230 PHE 0.011 0.001 PHE M 183 TYR 0.012 0.002 TYR P 38 ARG 0.005 0.001 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 3.245 Fit side-chains revert: symmetry clash REVERT: K 146 MET cc_start: 0.9045 (mtp) cc_final: 0.8829 (mtp) REVERT: O 106 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8575 (ttmt) REVERT: R 41 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7956 (mtm180) outliers start: 16 outliers final: 8 residues processed: 192 average time/residue: 3.0662 time to fit residues: 742.9973 Evaluate side-chains 204 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain R residue 41 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 313 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 377 optimal weight: 0.5980 chunk 407 optimal weight: 2.9990 chunk 336 optimal weight: 2.9990 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 302 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 ASN R 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 81899 Z= 0.212 Angle : 0.571 14.115 125756 Z= 0.321 Chirality : 0.035 0.880 16450 Planarity : 0.007 0.132 4636 Dihedral : 22.285 177.205 46007 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 1.59 % Allowed : 15.18 % Favored : 83.23 % 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: 0.47 (0.25), residues: 1163 helix: 1.33 (0.33), residues: 272 sheet: 0.88 (0.39), residues: 174 loop : -0.20 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.013 0.001 TYR P 38 ARG 0.004 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 3.267 Fit side-chains revert: symmetry clash REVERT: M 194 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8200 (mppt) REVERT: O 106 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8570 (ttmt) outliers start: 15 outliers final: 9 residues processed: 201 average time/residue: 3.0610 time to fit residues: 778.0877 Evaluate side-chains 199 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain N residue 58 ASN Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain R residue 25 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.0523 > 50: distance: 135 - 550: 3.210 distance: 171 - 553: 7.519 distance: 174 - 582: 7.223 distance: 275 - 528: 8.279 distance: 287 - 380: 3.004 distance: 297 - 531: 5.656 distance: 300 - 566: 9.564 distance: 334 - 569: 6.850 distance: 411 - 448: 14.200 distance: 428 - 486: 12.530 distance: 439 - 448: 13.322 distance: 440 - 496: 7.455 distance: 448 - 449: 15.274 distance: 448 - 456: 9.538 distance: 449 - 450: 17.301 distance: 449 - 452: 12.270 distance: 449 - 457: 12.503 distance: 450 - 451: 17.450 distance: 450 - 467: 37.366 distance: 452 - 453: 12.452 distance: 452 - 458: 4.020 distance: 452 - 459: 6.980 distance: 453 - 455: 8.929 distance: 453 - 460: 6.190 distance: 454 - 461: 9.619 distance: 454 - 462: 7.579 distance: 454 - 463: 8.760 distance: 455 - 464: 13.553 distance: 455 - 465: 15.771 distance: 455 - 466: 22.498 distance: 467 - 468: 17.387 distance: 467 - 475: 25.841 distance: 468 - 469: 10.626 distance: 468 - 471: 6.687 distance: 468 - 476: 7.535 distance: 469 - 470: 9.537 distance: 469 - 486: 8.555 distance: 471 - 472: 12.681 distance: 471 - 473: 8.858 distance: 471 - 477: 13.870 distance: 472 - 474: 7.535 distance: 472 - 478: 4.230 distance: 472 - 479: 13.203 distance: 473 - 480: 8.544 distance: 473 - 481: 8.907 distance: 473 - 482: 5.411 distance: 474 - 483: 4.011 distance: 474 - 484: 3.974 distance: 474 - 485: 5.464 distance: 486 - 487: 6.330 distance: 486 - 491: 4.333 distance: 487 - 488: 12.136 distance: 487 - 490: 5.087 distance: 487 - 492: 9.716 distance: 488 - 489: 9.746 distance: 488 - 496: 11.744 distance: 490 - 493: 14.013 distance: 490 - 494: 19.615 distance: 490 - 495: 10.127 distance: 496 - 507: 4.491 distance: 497 - 500: 3.105 distance: 497 - 508: 6.596 distance: 498 - 499: 12.523 distance: 498 - 516: 9.927 distance: 500 - 509: 11.604 distance: 500 - 510: 7.501 distance: 501 - 502: 5.621 distance: 502 - 504: 5.826 distance: 502 - 511: 4.401 distance: 503 - 505: 4.816 distance: 503 - 512: 8.433 distance: 504 - 506: 4.868 distance: 504 - 513: 3.994 distance: 505 - 506: 8.171 distance: 505 - 514: 6.466 distance: 506 - 515: 6.119 distance: 516 - 517: 6.006 distance: 516 - 524: 9.508 distance: 517 - 518: 5.693 distance: 517 - 520: 3.768 distance: 517 - 525: 5.904 distance: 518 - 519: 4.180 distance: 518 - 528: 6.857 distance: 520 - 521: 10.099 distance: 520 - 526: 12.143 distance: 520 - 527: 10.136 distance: 521 - 522: 6.213 distance: 521 - 523: 9.288 distance: 528 - 537: 7.312 distance: 529 - 530: 4.129 distance: 529 - 532: 6.608 distance: 529 - 538: 7.207 distance: 530 - 531: 9.720 distance: 530 - 550: 6.346 distance: 532 - 539: 4.933 distance: 532 - 540: 9.421 distance: 533 - 534: 6.949 distance: 533 - 541: 6.595 distance: 533 - 542: 5.992 distance: 534 - 535: 4.137 distance: 534 - 543: 9.748 distance: 534 - 544: 8.669 distance: 535 - 536: 6.502 distance: 535 - 545: 4.461 distance: 535 - 546: 8.396 distance: 536 - 547: 8.020 distance: 536 - 548: 10.223 distance: 536 - 549: 11.370 distance: 550 - 551: 7.162 distance: 550 - 557: 8.445 distance: 551 - 552: 5.489 distance: 551 - 554: 4.670 distance: 551 - 558: 7.319 distance: 552 - 553: 6.058 distance: 552 - 566: 10.888 distance: 554 - 555: 5.574 distance: 554 - 556: 6.135 distance: 554 - 559: 3.831 distance: 555 - 560: 9.202 distance: 555 - 561: 13.824 distance: 555 - 562: 9.843 distance: 556 - 563: 14.426 distance: 556 - 564: 10.874 distance: 556 - 565: 3.913 distance: 566 - 567: 7.778 distance: 566 - 573: 4.425 distance: 567 - 568: 5.204 distance: 567 - 570: 6.431 distance: 567 - 574: 6.334 distance: 568 - 569: 3.956 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