Starting phenix.real_space_refine on Sat Jul 20 05:00:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/07_2024/7yfc_33785.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/07_2024/7yfc_33785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/07_2024/7yfc_33785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/07_2024/7yfc_33785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/07_2024/7yfc_33785.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfc_33785/07_2024/7yfc_33785.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 6294 2.51 5 N 1686 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 182": "OE1" <-> "OE2" Residue "R TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9882 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1912 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1799 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2096 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.23, per 1000 atoms: 0.63 Number of scatterers: 9882 At special positions: 0 Unit cell: (88.88, 126.72, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1843 8.00 N 1686 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " 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=0, symmetry=0 Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 34.9% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 4.004A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.592A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.567A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.287A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 4.087A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.522A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.503A pdb=" N SER C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 56 removed outlier: 3.938A pdb=" N GLY C 56 " --> pdb=" O SER C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.990A pdb=" N VAL C 224 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.749A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.192A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 43 Processing helix chain 'R' and resid 48 through 76 removed outlier: 4.471A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 Processing helix chain 'R' and resid 118 through 124 Processing helix chain 'R' and resid 131 through 155 removed outlier: 3.570A pdb=" N TRP R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 171 through 181 Processing helix chain 'R' and resid 183 through 204 Processing helix chain 'R' and resid 300 through 329 removed outlier: 4.010A pdb=" N LEU R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 4.073A pdb=" N ILE R 324 " --> pdb=" O SER R 320 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 358 removed outlier: 3.796A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 359 through 362 removed outlier: 4.115A pdb=" N HIS R 362 " --> pdb=" O PRO R 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 359 through 362' Processing helix chain 'R' and resid 364 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.586A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.235A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.823A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.719A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.514A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.905A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.504A pdb=" N GLY B 244 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.687A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.769A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.407A pdb=" N PHE C 110 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.567A pdb=" N ARG C 160 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 146 through 148 removed outlier: 3.653A pdb=" N GLU C 246 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 189 " --> pdb=" O TRP C 176 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU C 187 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.009A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1332 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: 3.09 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1590 1.27 - 1.40: 2602 1.40 - 1.54: 5747 1.54 - 1.68: 73 1.68 - 1.81: 85 Bond restraints: 10097 Sorted by residual: bond pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 1.492 1.218 0.274 5.00e-02 4.00e+02 2.99e+01 bond pdb=" N PRO R 355 " pdb=" CA PRO R 355 " ideal model delta sigma weight residual 1.471 1.521 -0.050 1.32e-02 5.74e+03 1.43e+01 bond pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.51e+00 bond pdb=" C3 CLR R 602 " pdb=" O1 CLR R 602 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.09e+00 ... (remaining 10092 not shown) Histogram of bond angle deviations from ideal: 71.73 - 84.43: 2 84.43 - 97.12: 0 97.12 - 109.81: 1188 109.81 - 122.50: 11112 122.50 - 135.19: 1391 Bond angle restraints: 13693 Sorted by residual: angle pdb=" N PRO R 355 " pdb=" CD PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 103.20 74.58 28.62 1.50e+00 4.44e-01 3.64e+02 angle pdb=" CA PRO R 355 " pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 104.50 71.73 32.77 1.90e+00 2.77e-01 2.97e+02 angle pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 112.00 102.69 9.31 1.40e+00 5.10e-01 4.42e+01 angle pdb=" N PRO R 355 " pdb=" CA PRO R 355 " pdb=" CB PRO R 355 " ideal model delta sigma weight residual 103.48 97.38 6.10 1.00e+00 1.00e+00 3.73e+01 angle pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 106.10 125.14 -19.04 3.20e+00 9.77e-02 3.54e+01 ... (remaining 13688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 5332 22.39 - 44.78: 585 44.78 - 67.17: 75 67.17 - 89.56: 22 89.56 - 111.95: 2 Dihedral angle restraints: 6016 sinusoidal: 2358 harmonic: 3658 Sorted by residual: dihedral pdb=" N PRO R 355 " pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " pdb=" CB PRO R 355 " ideal model delta sinusoidal sigma weight residual 30.00 91.78 -61.78 1 1.50e+01 4.44e-03 2.25e+01 dihedral pdb=" C2 CLR R 602 " pdb=" C3 CLR R 602 " pdb=" C4 CLR R 602 " pdb=" C5 CLR R 602 " ideal model delta sinusoidal sigma weight residual -55.03 56.92 -111.95 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C5 CLR R 602 " pdb=" C3 CLR R 602 " pdb=" C4 CLR R 602 " pdb=" O1 CLR R 602 " ideal model delta sinusoidal sigma weight residual 175.64 64.31 111.33 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 6013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1275 0.051 - 0.102: 224 0.102 - 0.153: 42 0.153 - 0.204: 1 0.204 - 0.255: 1 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA TYR C 235 " pdb=" N TYR C 235 " pdb=" C TYR C 235 " pdb=" CB TYR C 235 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA THR B 181 " pdb=" N THR B 181 " pdb=" C THR B 181 " pdb=" CB THR B 181 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1540 not shown) Planarity restraints: 1731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 354 " 0.037 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO R 355 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 40 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO C 41 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 235 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO C 236 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.025 5.00e-02 4.00e+02 ... (remaining 1728 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 688 2.74 - 3.28: 9272 3.28 - 3.82: 16074 3.82 - 4.36: 18907 4.36 - 4.90: 34512 Nonbonded interactions: 79453 Sorted by model distance: nonbonded pdb=" NH1 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.198 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.239 2.440 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ASP A 335 " model vdw 2.273 2.520 nonbonded pdb=" OD1 ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.279 2.440 nonbonded pdb=" NH2 ARG C 180 " pdb=" OE2 GLU C 222 " model vdw 2.297 2.520 ... (remaining 79448 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=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: 2.860 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: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 30.650 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 0.371 10097 Z= 0.378 Angle : 0.658 32.766 13693 Z= 0.356 Chirality : 0.040 0.255 1543 Planarity : 0.004 0.054 1731 Dihedral : 18.014 111.951 3645 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.09 % Allowed : 31.36 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1240 helix: 2.54 (0.26), residues: 394 sheet: 0.47 (0.29), residues: 316 loop : -0.57 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 316 HIS 0.003 0.001 HIS B 311 PHE 0.015 0.001 PHE A 189 TYR 0.021 0.001 TYR C 235 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.138 Fit side-chains REVERT: B 42 ARG cc_start: 0.7413 (mmp-170) cc_final: 0.7086 (tpp-160) REVERT: R 353 VAL cc_start: 0.6955 (t) cc_final: 0.6711 (p) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 1.2016 time to fit residues: 156.5001 Evaluate side-chains 109 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 349 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0570 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10097 Z= 0.229 Angle : 0.555 11.911 13693 Z= 0.286 Chirality : 0.041 0.212 1543 Planarity : 0.004 0.048 1731 Dihedral : 5.417 42.520 1442 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.98 % Allowed : 29.11 % Favored : 65.92 % 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: 0.93 (0.24), residues: 1240 helix: 2.34 (0.26), residues: 405 sheet: 0.30 (0.29), residues: 326 loop : -0.56 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS A 324 PHE 0.016 0.001 PHE A 189 TYR 0.028 0.001 TYR C 235 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 107 time to evaluate : 1.070 Fit side-chains REVERT: B 59 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: B 197 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6151 (mtp-110) REVERT: B 234 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7476 (t80) REVERT: B 336 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7991 (tt) REVERT: R 75 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7580 (t-170) outliers start: 53 outliers final: 22 residues processed: 145 average time/residue: 1.1095 time to fit residues: 173.9382 Evaluate side-chains 134 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 127 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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: 72.0617 > 50: distance: 57 - 107: 35.397 distance: 85 - 91: 28.144 distance: 91 - 92: 14.890 distance: 92 - 93: 39.642 distance: 93 - 94: 39.331 distance: 95 - 96: 31.482 distance: 95 - 97: 25.969 distance: 98 - 99: 34.310 distance: 98 - 156: 40.760 distance: 99 - 100: 52.521 distance: 99 - 102: 7.485 distance: 100 - 101: 34.149 distance: 100 - 104: 20.068 distance: 101 - 153: 14.575 distance: 102 - 103: 40.823 distance: 104 - 105: 38.092 distance: 105 - 106: 50.862 distance: 105 - 108: 51.339 distance: 106 - 107: 64.015 distance: 106 - 109: 11.268 distance: 109 - 110: 68.084 distance: 109 - 139: 58.233 distance: 110 - 111: 62.604 distance: 110 - 113: 46.629 distance: 111 - 112: 42.969 distance: 111 - 115: 24.659 distance: 113 - 114: 42.810 distance: 115 - 116: 38.737 distance: 116 - 117: 55.839 distance: 116 - 119: 55.894 distance: 117 - 118: 48.599 distance: 117 - 124: 6.677 distance: 119 - 120: 40.604 distance: 121 - 122: 55.805 distance: 124 - 125: 35.912 distance: 125 - 126: 56.910 distance: 125 - 128: 39.600 distance: 126 - 127: 56.285 distance: 126 - 132: 41.282 distance: 128 - 129: 56.700 distance: 129 - 131: 38.788 distance: 132 - 133: 55.591 distance: 133 - 134: 39.979 distance: 134 - 135: 64.262 distance: 134 - 136: 48.952 distance: 137 - 138: 40.416 distance: 137 - 140: 70.220 distance: 138 - 145: 68.466 distance: 140 - 141: 11.066 distance: 141 - 142: 32.876 distance: 143 - 144: 41.478 distance: 146 - 147: 39.518 distance: 146 - 149: 69.518 distance: 147 - 148: 39.297 distance: 147 - 153: 58.194 distance: 149 - 150: 55.071 distance: 150 - 151: 37.226 distance: 150 - 152: 16.901 distance: 153 - 154: 43.878 distance: 154 - 155: 40.869 distance: 154 - 157: 39.267 distance: 155 - 156: 40.549 distance: 155 - 161: 33.352 distance: 157 - 158: 43.605 distance: 157 - 159: 40.631 distance: 158 - 160: 44.545