Starting phenix.real_space_refine on Fri Jun 28 14:31:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/06_2024/7zxy_15017_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/06_2024/7zxy_15017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/06_2024/7zxy_15017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/06_2024/7zxy_15017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/06_2024/7zxy_15017_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/06_2024/7zxy_15017_updated.pdb" } resolution = 3.15 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= 0.001 sd= 0.007 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 Fe 12 7.16 5 P 7 5.49 5 Mg 2 5.21 5 S 76 5.16 5 C 10361 2.51 5 N 2417 2.21 5 O 2731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 148": "OD1" <-> "OD2" Residue "I GLU 180": "OE1" <-> "OE2" Residue "J ASP 35": "OD1" <-> "OD2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K GLU 282": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 15606 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1750 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "B" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1211 Classifications: {'peptide': 158} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 140} Chain: "C" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2116 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "D" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1248 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain breaks: 1 Chain: "E" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 267 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "H" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 235 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1750 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "J" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1223 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2116 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1248 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain breaks: 1 Chain: "M" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 248 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "O" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "P" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 235 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'ECH': 1, 'HEC': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'CLA': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'HEC': 1, 'LFA': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 221 Unusual residues: {'ECH': 1, 'HEC': 1, 'HEM': 2, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 211 Unusual residues: {'CLA': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5796 SG CYS D 120 78.989 77.612 95.772 1.00 30.79 S ATOM 5936 SG CYS D 138 76.370 80.248 96.868 1.00 33.12 S ATOM 13144 SG CYS L 120 34.375 76.130 50.594 1.00 30.90 S ATOM 13284 SG CYS L 138 37.537 74.579 48.855 1.00 31.82 S Time building chain proxies: 8.60, per 1000 atoms: 0.55 Number of scatterers: 15606 At special positions: 0 Unit cell: (114.48, 128.26, 139.92, 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) Fe 12 26.01 S 76 16.00 P 7 15.00 Mg 2 11.99 O 2731 8.00 N 2417 7.00 C 10361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 140 " distance=2.03 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 201 " pdb="FE1 FES D 201 " - pdb=" ND1 HIS D 122 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 138 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 120 " pdb="FE1 FES D 201 " - pdb=" ND1 HIS D 141 " pdb=" FES L 201 " pdb="FE1 FES L 201 " - pdb=" ND1 HIS L 141 " pdb="FE1 FES L 201 " - pdb=" ND1 HIS L 122 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 138 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 120 " Number of angles added : 6 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 13 sheets defined 45.3% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 3.868A pdb=" N TRP A 14 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 16 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 39 through 63 removed outlier: 4.403A pdb=" N GLY A 44 " --> pdb=" O TYR A 41 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 57 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY A 58 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 122 through 144 removed outlier: 4.399A pdb=" N SER A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 40 through 57 Processing helix chain 'B' and resid 79 through 90 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 94 through 108 removed outlier: 3.993A pdb=" N ILE B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 127 through 148 removed outlier: 3.994A pdb=" N THR B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 248 through 282 Processing helix chain 'D' and resid 25 through 54 Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 78 through 81 No H-bonds generated for 'chain 'D' and resid 78 through 81' Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'E' and resid 3 through 28 Processing helix chain 'F' and resid 8 through 31 Processing helix chain 'G' and resid 4 through 29 Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 4 through 25 Processing helix chain 'I' and resid 11 through 19 removed outlier: 3.949A pdb=" N ASP I 17 " --> pdb=" O TRP I 14 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU I 19 " --> pdb=" O ASN I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 30 Processing helix chain 'I' and resid 39 through 63 removed outlier: 4.440A pdb=" N GLY I 44 " --> pdb=" O TYR I 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY I 45 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR I 57 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY I 58 " --> pdb=" O PHE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 81 Processing helix chain 'I' and resid 86 through 114 Processing helix chain 'I' and resid 122 through 143 Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 169 through 177 Processing helix chain 'I' and resid 184 through 195 Processing helix chain 'I' and resid 197 through 216 Processing helix chain 'J' and resid 12 through 20 Processing helix chain 'J' and resid 40 through 57 Processing helix chain 'J' and resid 79 through 90 Proline residue: J 83 - end of helix removed outlier: 4.121A pdb=" N ILE J 90 " --> pdb=" O ILE J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 109 removed outlier: 3.971A pdb=" N ILE J 104 " --> pdb=" O GLY J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix Processing helix chain 'J' and resid 111 through 114 No H-bonds generated for 'chain 'J' and resid 111 through 114' Processing helix chain 'J' and resid 123 through 125 No H-bonds generated for 'chain 'J' and resid 123 through 125' Processing helix chain 'J' and resid 127 through 148 removed outlier: 3.952A pdb=" N THR J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 8 Processing helix chain 'K' and resid 21 through 24 Processing helix chain 'K' and resid 92 through 98 Processing helix chain 'K' and resid 248 through 283 Processing helix chain 'L' and resid 25 through 54 Proline residue: L 49 - end of helix Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'M' and resid 3 through 28 Processing helix chain 'N' and resid 8 through 32 Processing helix chain 'O' and resid 4 through 29 Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 3 through 25 Processing sheet with id= A, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.635A pdb=" N VAL C 49 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 39 through 41 removed outlier: 8.359A pdb=" N VAL C 40 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL C 244 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.548A pdb=" N HIS C 150 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 183 through 185 Processing sheet with id= E, first strand: chain 'D' and resid 89 through 94 removed outlier: 3.709A pdb=" N VAL D 91 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 116 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 128 through 130 Processing sheet with id= G, first strand: chain 'D' and resid 163 through 166 Processing sheet with id= H, first strand: chain 'K' and resid 33 through 35 Processing sheet with id= I, first strand: chain 'K' and resid 39 through 41 removed outlier: 8.014A pdb=" N VAL K 40 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL K 244 " --> pdb=" O VAL K 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 191 through 193 Processing sheet with id= K, first strand: chain 'L' and resid 90 through 94 Processing sheet with id= L, first strand: chain 'L' and resid 128 through 130 Processing sheet with id= M, first strand: chain 'L' and resid 163 through 165 696 hydrogen bonds defined for protein. 1869 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: 5.18 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 6385 1.41 - 1.61: 9459 1.61 - 1.81: 132 1.81 - 2.01: 8 2.01 - 2.20: 48 Bond restraints: 16032 Sorted by residual: bond pdb=" CAC HEC I 305 " pdb=" CBC HEC I 305 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC I 305 " pdb=" C3D HEC I 305 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC A 304 " pdb=" C3D HEC A 304 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CAB HEC I 305 " pdb=" CBB HEC I 305 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAC HEC A 304 " pdb=" CBC HEC A 304 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 16027 not shown) Histogram of bond angle deviations from ideal: 75.26 - 96.13: 44 96.13 - 116.99: 11340 116.99 - 137.86: 10482 137.86 - 158.72: 2 158.72 - 179.59: 20 Bond angle restraints: 21888 Sorted by residual: angle pdb=" C3C HEC I 305 " pdb=" CAC HEC I 305 " pdb=" CBC HEC I 305 " ideal model delta sigma weight residual 109.00 125.33 -16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" C3B HEC I 305 " pdb=" CAB HEC I 305 " pdb=" CBB HEC I 305 " ideal model delta sigma weight residual 109.00 124.21 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O11 PGV B 202 " pdb=" P PGV B 202 " pdb=" O12 PGV B 202 " ideal model delta sigma weight residual 92.97 107.50 -14.53 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C3B HEC A 304 " pdb=" CAB HEC A 304 " pdb=" CBB HEC A 304 " ideal model delta sigma weight residual 109.00 123.45 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C3C HEC A 304 " pdb=" CAC HEC A 304 " pdb=" CBC HEC A 304 " ideal model delta sigma weight residual 109.00 123.38 -14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 21883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.91: 8981 32.91 - 65.82: 225 65.82 - 98.74: 44 98.74 - 131.65: 2 131.65 - 164.56: 7 Dihedral angle restraints: 9259 sinusoidal: 3858 harmonic: 5401 Sorted by residual: dihedral pdb=" C2B HEC A 304 " pdb=" C3B HEC A 304 " pdb=" CAB HEC A 304 " pdb=" CBB HEC A 304 " ideal model delta sinusoidal sigma weight residual 60.00 -29.50 89.50 2 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" C2B HEC I 305 " pdb=" C3B HEC I 305 " pdb=" CAB HEC I 305 " pdb=" CBB HEC I 305 " ideal model delta sinusoidal sigma weight residual 60.00 -21.71 81.71 2 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" C2C HEC I 305 " pdb=" C3C HEC I 305 " pdb=" CAC HEC I 305 " pdb=" CBC HEC I 305 " ideal model delta sinusoidal sigma weight residual 60.00 0.17 59.83 2 1.00e+01 1.00e-02 3.59e+01 ... (remaining 9256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1786 0.047 - 0.095: 477 0.095 - 0.142: 107 0.142 - 0.189: 8 0.189 - 0.237: 7 Chirality restraints: 2385 Sorted by residual: chirality pdb=" C05 PGV C 303 " pdb=" C04 PGV C 303 " pdb=" C06 PGV C 303 " pdb=" O05 PGV C 303 " both_signs ideal model delta sigma weight residual False 2.29 2.53 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C05 PGV B 203 " pdb=" C04 PGV B 203 " pdb=" C06 PGV B 203 " pdb=" O05 PGV B 203 " both_signs ideal model delta sigma weight residual False 2.29 2.53 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C05 PGV J 204 " pdb=" C04 PGV J 204 " pdb=" C06 PGV J 204 " pdb=" O05 PGV J 204 " both_signs ideal model delta sigma weight residual False 2.29 2.53 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2382 not shown) Planarity restraints: 2705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " -0.014 2.00e-02 2.50e+03 3.31e-02 2.47e+01 pdb=" C2C HEC C 301 " 0.090 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " -0.003 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " -0.020 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " -0.015 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " 0.001 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 301 " -0.011 2.00e-02 2.50e+03 3.04e-02 2.08e+01 pdb=" C2C HEC K 301 " 0.083 2.00e-02 2.50e+03 pdb=" C3C HEC K 301 " -0.003 2.00e-02 2.50e+03 pdb=" C4C HEC K 301 " -0.001 2.00e-02 2.50e+03 pdb=" CAC HEC K 301 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEC K 301 " -0.016 2.00e-02 2.50e+03 pdb=" CHD HEC K 301 " 0.001 2.00e-02 2.50e+03 pdb=" CMC HEC K 301 " -0.025 2.00e-02 2.50e+03 pdb=" NC HEC K 301 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 86 " -0.052 5.00e-02 4.00e+02 7.93e-02 1.00e+01 pdb=" N PRO C 87 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " -0.043 5.00e-02 4.00e+02 ... (remaining 2702 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 287 2.66 - 3.22: 14805 3.22 - 3.78: 25405 3.78 - 4.34: 35580 4.34 - 4.90: 58163 Nonbonded interactions: 134240 Sorted by model distance: nonbonded pdb=" NE2 HIS I 93 " pdb="FE HEM I 303 " model vdw 2.106 3.080 nonbonded pdb=" NE2 HIS I 209 " pdb="FE HEM I 304 " model vdw 2.170 3.080 nonbonded pdb=" OH TYR I 65 " pdb=" O LEU I 145 " model vdw 2.201 2.440 nonbonded pdb=" NE2 HIS A 209 " pdb="FE HEM A 303 " model vdw 2.210 3.080 nonbonded pdb=" O PHE I 59 " pdb=" OG1 THR I 62 " model vdw 2.211 2.440 ... (remaining 134235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 222 or resid 301 or resid 303)) selection = (chain 'I' and (resid 3 through 222 or resid 301 or resid 303)) } ncs_group { reference = (chain 'B' and (resid 2 through 159 or (resid 202 and (name C01 or name C02 or n \ ame C03 or name C04 or name C05 or name C06 or name C1 or name C10 or name C11 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O \ 03 or name O04 or name O05 or name O06 or name O11 or name O12 or name O13 or na \ me O14 or name P )) or resid 203)) selection = (chain 'J' and (resid 2 through 159 or (resid 203 and (name C01 or name C02 or n \ ame C03 or name C04 or name C05 or name C06 or name C1 or name C10 or name C11 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O \ 03 or name O04 or name O05 or name O06 or name O11 or name O12 or name O13 or na \ me O14 or name P )) or (resid 204 and (name C01 or name C02 or name C03 or name \ C04 or name C05 or name C06 or name C1 or name C10 or name C11 or name C19 or na \ me C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C4 or name C5 or name C6 or name C7 \ or name C8 or name C9 or name O01 or name O02 or name O03 or name O04 or name O \ 05 or name O06 or name O11 or name O12 or name O13 or name O14 or name P )))) } ncs_group { reference = (chain 'C' and (resid 1 through 285 or resid 301)) selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = (chain 'E' and resid 1 through 32) selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 34) selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 2.680 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.460 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.006 0.213 16032 Z= 0.366 Angle : 0.936 16.334 21888 Z= 0.402 Chirality : 0.046 0.237 2385 Planarity : 0.005 0.101 2705 Dihedral : 16.227 164.559 5810 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.44 (0.19), residues: 1873 helix: 0.96 (0.17), residues: 930 sheet: -1.75 (0.37), residues: 182 loop : -1.49 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP L 190 HIS 0.009 0.001 HIS I 209 PHE 0.044 0.002 PHE A 138 TYR 0.012 0.001 TYR B 80 ARG 0.007 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.626 Fit side-chains REVERT: A 103 MET cc_start: 0.8118 (mmp) cc_final: 0.7320 (mmt) REVERT: B 153 LYS cc_start: 0.8350 (ptpp) cc_final: 0.7941 (pttt) REVERT: K 138 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6841 (pttm) REVERT: P 14 LEU cc_start: 0.8789 (tp) cc_final: 0.8447 (tt) REVERT: P 21 MET cc_start: 0.8176 (mmp) cc_final: 0.7906 (mmp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2811 time to fit residues: 95.9373 Evaluate side-chains 209 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.0370 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 142 optimal weight: 0.0570 chunk 55 optimal weight: 30.0000 chunk 86 optimal weight: 0.0170 chunk 106 optimal weight: 0.0670 chunk 165 optimal weight: 4.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16032 Z= 0.170 Angle : 0.648 20.121 21888 Z= 0.256 Chirality : 0.041 0.161 2385 Planarity : 0.004 0.054 2705 Dihedral : 14.986 157.688 2498 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.26 % Allowed : 5.60 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.18 (0.19), residues: 1873 helix: 1.24 (0.17), residues: 922 sheet: -1.71 (0.37), residues: 182 loop : -1.39 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 190 HIS 0.005 0.001 HIS I 209 PHE 0.021 0.001 PHE A 12 TYR 0.012 0.001 TYR C 102 ARG 0.005 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 220 time to evaluate : 1.592 Fit side-chains REVERT: A 103 MET cc_start: 0.8214 (mmp) cc_final: 0.7425 (mmt) REVERT: B 130 MET cc_start: 0.8887 (mmp) cc_final: 0.8659 (mmp) REVERT: B 153 LYS cc_start: 0.8377 (ptpp) cc_final: 0.7992 (pttt) REVERT: K 138 LYS cc_start: 0.7106 (mtmt) cc_final: 0.6866 (pttm) REVERT: P 14 LEU cc_start: 0.8849 (tp) cc_final: 0.8484 (tt) REVERT: P 21 MET cc_start: 0.8091 (mmp) cc_final: 0.7839 (mmp) outliers start: 4 outliers final: 1 residues processed: 222 average time/residue: 0.2610 time to fit residues: 86.4983 Evaluate side-chains 208 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.0020 chunk 165 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16032 Z= 0.179 Angle : 0.651 23.074 21888 Z= 0.249 Chirality : 0.041 0.157 2385 Planarity : 0.004 0.048 2705 Dihedral : 14.064 170.929 2498 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.45 % Allowed : 7.21 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.00 (0.19), residues: 1873 helix: 1.36 (0.17), residues: 922 sheet: -1.76 (0.38), residues: 172 loop : -1.23 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 153 HIS 0.006 0.001 HIS I 209 PHE 0.022 0.001 PHE A 12 TYR 0.008 0.001 TYR A 78 ARG 0.003 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 1.634 Fit side-chains REVERT: A 13 GLN cc_start: 0.7991 (mt0) cc_final: 0.7633 (mt0) REVERT: A 103 MET cc_start: 0.8251 (mmp) cc_final: 0.7503 (mmt) REVERT: A 138 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7727 (t80) REVERT: B 153 LYS cc_start: 0.8403 (ptpp) cc_final: 0.8017 (pttt) REVERT: I 103 MET cc_start: 0.8233 (mmt) cc_final: 0.7657 (mmp) REVERT: P 21 MET cc_start: 0.8091 (mmp) cc_final: 0.7864 (mmp) outliers start: 7 outliers final: 4 residues processed: 220 average time/residue: 0.2702 time to fit residues: 88.0371 Evaluate side-chains 210 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 205 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.7904 > 50: distance: 60 - 109: 24.476 distance: 63 - 106: 27.294 distance: 75 - 94: 14.065 distance: 78 - 91: 6.812 distance: 85 - 91: 3.259 distance: 91 - 92: 8.764 distance: 92 - 93: 11.077 distance: 92 - 95: 10.398 distance: 93 - 94: 10.348 distance: 93 - 98: 14.523 distance: 95 - 96: 7.456 distance: 95 - 97: 17.486 distance: 98 - 99: 7.733 distance: 99 - 100: 13.307 distance: 99 - 102: 13.188 distance: 100 - 101: 3.915 distance: 100 - 106: 5.493 distance: 102 - 103: 3.185 distance: 103 - 104: 12.979 distance: 103 - 105: 7.880 distance: 106 - 107: 20.052 distance: 107 - 108: 13.855 distance: 107 - 110: 10.806 distance: 108 - 109: 30.707 distance: 108 - 112: 11.644 distance: 110 - 111: 7.632 distance: 112 - 113: 21.883 distance: 113 - 114: 26.819 distance: 113 - 116: 14.292 distance: 114 - 115: 33.785 distance: 114 - 119: 42.703 distance: 116 - 117: 14.137 distance: 116 - 118: 24.027 distance: 119 - 120: 9.728 distance: 120 - 121: 10.181 distance: 120 - 123: 4.098 distance: 121 - 122: 13.166 distance: 121 - 133: 8.093 distance: 123 - 124: 15.951 distance: 124 - 125: 7.985 distance: 124 - 126: 3.566 distance: 125 - 127: 7.706 distance: 126 - 128: 9.241 distance: 126 - 129: 5.208 distance: 127 - 128: 3.307 distance: 128 - 130: 4.706 distance: 129 - 131: 5.969 distance: 130 - 132: 6.080 distance: 131 - 132: 9.171 distance: 133 - 134: 16.279 distance: 134 - 135: 5.047 distance: 134 - 137: 10.321 distance: 135 - 136: 6.084 distance: 135 - 140: 3.720 distance: 137 - 138: 5.785 distance: 137 - 139: 21.649 distance: 140 - 141: 19.079 distance: 141 - 142: 9.280 distance: 141 - 144: 4.074 distance: 142 - 143: 9.856 distance: 142 - 149: 7.646 distance: 144 - 145: 5.067 distance: 145 - 146: 3.830 distance: 146 - 147: 5.842 distance: 146 - 148: 10.875 distance: 149 - 150: 17.675 distance: 150 - 151: 10.927 distance: 150 - 153: 12.879 distance: 151 - 152: 8.618 distance: 151 - 156: 3.778 distance: 153 - 154: 19.972 distance: 153 - 155: 15.332 distance: 156 - 157: 14.379 distance: 157 - 158: 34.317 distance: 157 - 160: 24.962 distance: 158 - 159: 23.517 distance: 158 - 164: 8.926 distance: 160 - 161: 14.531 distance: 161 - 162: 24.547 distance: 161 - 163: 9.251 distance: 164 - 165: 27.486 distance: 165 - 166: 17.201 distance: 165 - 168: 10.628 distance: 166 - 167: 15.955 distance: 166 - 175: 8.327 distance: 168 - 169: 12.228 distance: 169 - 170: 9.728 distance: 169 - 171: 5.985 distance: 170 - 172: 4.305 distance: 171 - 173: 8.778 distance: 172 - 174: 4.323 distance: 173 - 174: 7.785