Starting phenix.real_space_refine (version: dev) on Sun Mar 12 23:42:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/03_2023/7eo4_31226_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/03_2023/7eo4_31226.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/03_2023/7eo4_31226_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/03_2023/7eo4_31226_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/03_2023/7eo4_31226_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/03_2023/7eo4_31226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/03_2023/7eo4_31226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/03_2023/7eo4_31226_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/03_2023/7eo4_31226_neut_updated.pdb" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.078 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 Process input model Symmetric amino acids flipped Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 8302 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2247 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1205 Classifications: {'peptide': 151} Link IDs: {'TRANS': 150} Chain breaks: 4 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'J8C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.98, per 1000 atoms: 0.60 Number of scatterers: 8302 At special positions: 0 Unit cell: (93.5, 123.2, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 F 3 9.00 O 1531 8.00 N 1399 7.00 C 5311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 191 " distance=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.2 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 31.6% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 Processing helix chain 'A' and resid 47 through 71 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 79 through 104 removed outlier: 3.615A pdb=" N VAL A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 114 through 145 removed outlier: 4.004A pdb=" N ALA A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.644A pdb=" N GLY A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 200 through 232 Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.938A pdb=" N ILE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.903A pdb=" N VAL A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 297 through 313 removed outlier: 3.777A pdb=" N ASN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.049A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 251 through 254 No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 329 through 350 removed outlier: 4.196A pdb=" N PHE B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.973A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing sheet with id= A, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.191A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 37 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.109A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.867A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.762A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.548A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.883A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C 253 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 295 through 297 removed outlier: 3.533A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.803A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.547A pdb=" N TRP E 36 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.505A pdb=" N CYS E 147 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE E 200 " --> pdb=" O CYS E 147 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.554A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 912 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: 2.53 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2587 1.34 - 1.46: 1992 1.46 - 1.58: 3806 1.58 - 1.71: 3 1.71 - 1.83: 81 Bond restraints: 8469 Sorted by residual: bond pdb=" C16 J8C A 401 " pdb=" C19 J8C A 401 " ideal model delta sigma weight residual 0.000 1.576 -1.576 2.00e-02 2.50e+03 6.21e+03 bond pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " ideal model delta sigma weight residual 1.958 1.584 0.374 2.00e-02 2.50e+03 3.49e+02 bond pdb=" C02 J8C A 401 " pdb=" C03 J8C A 401 " ideal model delta sigma weight residual 1.428 1.563 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C19 J8C A 401 " pdb=" C20 J8C A 401 " ideal model delta sigma weight residual 1.457 1.585 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" N10 J8C A 401 " pdb=" O11 J8C A 401 " ideal model delta sigma weight residual 1.523 1.408 0.115 2.00e-02 2.50e+03 3.33e+01 ... (remaining 8464 not shown) Histogram of bond angle deviations from ideal: 87.26 - 96.64: 4 96.64 - 106.02: 138 106.02 - 115.39: 5192 115.39 - 124.77: 5976 124.77 - 134.15: 162 Bond angle restraints: 11472 Sorted by residual: angle pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " pdb=" C14 J8C A 401 " ideal model delta sigma weight residual 105.15 120.45 -15.30 3.00e+00 1.11e-01 2.60e+01 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.76 5.41 1.14e+00 7.69e-01 2.25e+01 angle pdb=" N ASP C 303 " pdb=" CA ASP C 303 " pdb=" C ASP C 303 " ideal model delta sigma weight residual 107.48 117.67 -10.19 2.29e+00 1.91e-01 1.98e+01 angle pdb=" N ASP E 211 " pdb=" CA ASP E 211 " pdb=" C ASP E 211 " ideal model delta sigma weight residual 110.80 101.34 9.46 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N PHE C 292 " pdb=" CA PHE C 292 " pdb=" CB PHE C 292 " ideal model delta sigma weight residual 114.17 109.11 5.06 1.14e+00 7.69e-01 1.97e+01 ... (remaining 11467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 4718 22.93 - 45.86: 242 45.86 - 68.79: 25 68.79 - 91.72: 4 91.72 - 114.65: 4 Dihedral angle restraints: 4993 sinusoidal: 1928 harmonic: 3065 Sorted by residual: dihedral pdb=" C ASP E 211 " pdb=" N ASP E 211 " pdb=" CA ASP E 211 " pdb=" CB ASP E 211 " ideal model delta harmonic sigma weight residual -122.60 -112.23 -10.37 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" CA THR B 187 " pdb=" C THR B 187 " pdb=" N HIS B 188 " pdb=" CA HIS B 188 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP C 339 " pdb=" C TRP C 339 " pdb=" N ASN C 340 " pdb=" CA ASN C 340 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.173: 1323 1.173 - 2.347: 0 2.347 - 3.520: 0 3.520 - 4.693: 0 4.693 - 5.866: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" C33 J8C A 401 " pdb=" C32 J8C A 401 " pdb=" C34 J8C A 401 " pdb=" C35 J8C A 401 " both_signs ideal model delta sigma weight residual False -2.82 3.05 -5.87 2.00e-01 2.50e+01 8.60e+02 chirality pdb=" CA ASP E 211 " pdb=" N ASP E 211 " pdb=" C ASP E 211 " pdb=" CB ASP E 211 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ALA E 209 " pdb=" N ALA E 209 " pdb=" C ALA E 209 " pdb=" CB ALA E 209 " both_signs ideal model delta sigma weight residual False 2.48 2.74 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1321 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 292 " -0.291 9.50e-02 1.11e+02 1.31e-01 1.05e+01 pdb=" NE ARG A 292 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 292 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 292 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 292 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO C 236 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.61e+00 pdb=" N PRO A 178 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.039 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1250 2.76 - 3.29: 7641 3.29 - 3.83: 12511 3.83 - 4.36: 14972 4.36 - 4.90: 26009 Nonbonded interactions: 62383 Sorted by model distance: nonbonded pdb=" N GLY C 144 " pdb=" OD1 ASP C 163 " model vdw 2.220 2.520 nonbonded pdb=" O GLY E 197 " pdb=" OG1 THR E 198 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.244 2.440 nonbonded pdb=" O LEU C 30 " pdb=" OG1 THR C 34 " model vdw 2.274 2.440 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.297 2.440 ... (remaining 62378 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5311 2.51 5 N 1399 2.21 5 O 1531 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.760 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: 0.000 Extract box with map and model: 4.380 Check model and map are aligned: 0.100 Process input model: 23.960 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 1.576 8469 Z= 1.552 Angle : 1.004 15.296 11472 Z= 0.538 Chirality : 0.170 5.866 1324 Planarity : 0.007 0.131 1424 Dihedral : 14.001 114.647 3004 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.38 (0.25), residues: 1033 helix: 1.19 (0.29), residues: 312 sheet: -1.83 (0.30), residues: 239 loop : -1.84 (0.27), residues: 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.913 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 1.0828 time to fit residues: 200.2541 Evaluate side-chains 148 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 237 ASN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.124 8469 Z= 0.415 Angle : 1.161 25.280 11472 Z= 0.550 Chirality : 0.074 2.101 1324 Planarity : 0.007 0.068 1424 Dihedral : 8.611 108.632 1151 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.31 (0.25), residues: 1033 helix: 1.20 (0.29), residues: 311 sheet: -1.59 (0.30), residues: 249 loop : -1.88 (0.27), residues: 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 0.889 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 153 average time/residue: 1.0632 time to fit residues: 174.1744 Evaluate side-chains 159 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 7 residues processed: 10 average time/residue: 0.3260 time to fit residues: 5.1480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 75 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.124 8469 Z= 0.415 Angle : 1.161 25.280 11472 Z= 0.550 Chirality : 0.074 2.101 1324 Planarity : 0.007 0.068 1424 Dihedral : 8.611 108.632 1151 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.31 (0.25), residues: 1033 helix: 1.20 (0.29), residues: 311 sheet: -1.59 (0.30), residues: 249 loop : -1.88 (0.27), residues: 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.941 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 150 average time/residue: 1.0616 time to fit residues: 170.6703 Evaluate side-chains 149 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.3352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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: 70.6425 > 50: distance: 16 - 112: 25.368 distance: 19 - 109: 30.727 distance: 30 - 95: 31.114 distance: 33 - 92: 25.377 distance: 74 - 103: 37.277 distance: 77 - 100: 29.616 distance: 87 - 92: 28.428 distance: 92 - 93: 20.847 distance: 93 - 94: 55.508 distance: 93 - 96: 27.497 distance: 94 - 95: 57.594 distance: 94 - 100: 51.216 distance: 96 - 97: 30.488 distance: 97 - 98: 22.861 distance: 97 - 99: 46.890 distance: 100 - 101: 31.309 distance: 101 - 102: 38.233 distance: 101 - 104: 15.231 distance: 102 - 109: 57.673 distance: 104 - 105: 26.782 distance: 105 - 106: 19.235 distance: 106 - 107: 24.220 distance: 106 - 108: 35.624 distance: 109 - 110: 15.471 distance: 110 - 111: 38.765 distance: 110 - 113: 32.135 distance: 111 - 112: 50.833 distance: 111 - 117: 56.606 distance: 113 - 114: 47.662 distance: 114 - 115: 6.945 distance: 115 - 116: 43.386 distance: 117 - 118: 22.339 distance: 118 - 119: 20.612 distance: 118 - 121: 21.782 distance: 119 - 120: 19.314 distance: 119 - 124: 35.360 distance: 121 - 122: 27.086 distance: 121 - 123: 27.837 distance: 125 - 126: 44.340 distance: 125 - 128: 41.326 distance: 126 - 127: 43.012 distance: 126 - 130: 54.188 distance: 128 - 129: 52.600 distance: 130 - 131: 15.196 distance: 131 - 132: 24.483 distance: 131 - 134: 37.264 distance: 132 - 133: 63.145 distance: 132 - 138: 56.157 distance: 134 - 135: 18.284 distance: 135 - 136: 20.331 distance: 135 - 137: 24.378 distance: 138 - 139: 46.713 distance: 139 - 140: 32.234 distance: 139 - 142: 13.663 distance: 140 - 141: 44.660 distance: 140 - 149: 21.888 distance: 142 - 143: 16.582 distance: 144 - 145: 27.378 distance: 145 - 146: 43.062 distance: 146 - 147: 39.625 distance: 146 - 148: 42.893 distance: 149 - 150: 26.599 distance: 150 - 151: 35.334 distance: 150 - 153: 53.365 distance: 151 - 152: 56.681 distance: 151 - 155: 3.705 distance: 155 - 156: 45.443 distance: 156 - 157: 27.390 distance: 156 - 159: 33.013 distance: 157 - 158: 12.772 distance: 157 - 164: 22.919 distance: 159 - 160: 20.903 distance: 160 - 161: 20.812 distance: 161 - 162: 8.857 distance: 161 - 163: 8.031 distance: 164 - 165: 23.361 distance: 165 - 166: 4.308 distance: 165 - 168: 8.542 distance: 166 - 167: 52.649 distance: 166 - 172: 32.270 distance: 168 - 169: 39.350 distance: 169 - 170: 34.968 distance: 169 - 171: 42.083 distance: 179 - 186: 3.086