Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:26:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2022/7cx2_30489_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2022/7cx2_30489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2022/7cx2_30489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2022/7cx2_30489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2022/7cx2_30489_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2022/7cx2_30489_updated_updated.pdb" } resolution = 2.8 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= 0.009 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "R ARG 107": "NH1" <-> "NH2" Residue "R PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 150": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 319": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N ARG 105": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 7930 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2027 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1870 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.03, per 1000 atoms: 0.63 Number of scatterers: 7930 At special positions: 0 Unit cell: (77.064, 110.526, 125.736, 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 52 16.00 O 1477 8.00 N 1374 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 3.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 36.7% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'R' and resid 27 through 47 removed outlier: 3.924A pdb=" N GLY R 35 " --> pdb=" O MET R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 82 removed outlier: 3.859A pdb=" N GLU R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 94 removed outlier: 3.933A pdb=" N TYR R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 139 Processing helix chain 'R' and resid 141 through 147 Processing helix chain 'R' and resid 150 through 173 removed outlier: 3.793A pdb=" N LEU R 154 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 155 " --> pdb=" O GLY R 152 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU R 157 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Proline residue: R 158 - end of helix removed outlier: 3.556A pdb=" N LEU R 170 " --> pdb=" O PHE R 167 " (cutoff:3.500A) Proline residue: R 171 - end of helix Processing helix chain 'R' and resid 196 through 227 Processing helix chain 'R' and resid 259 through 276 Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 291 through 294 No H-bonds generated for 'chain 'R' and resid 291 through 294' Processing helix chain 'R' and resid 297 through 316 removed outlier: 3.821A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER R 305 " --> pdb=" O LEU R 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.663A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.543A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.899A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 4.001A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 23 removed outlier: 4.056A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 178 through 180 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.091A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.873A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.929A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.615A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.997A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.738A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.931A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 999 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: 2.06 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1293 1.31 - 1.44: 2222 1.44 - 1.57: 4495 1.57 - 1.70: 2 1.70 - 1.83: 74 Bond restraints: 8086 Sorted by residual: bond pdb=" C8 P2E R 401 " pdb=" C9 P2E R 401 " ideal model delta sigma weight residual 1.515 1.436 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C11 P2E R 401 " pdb=" O4 P2E R 401 " ideal model delta sigma weight residual 1.402 1.330 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C10 P2E R 401 " pdb=" C11 P2E R 401 " ideal model delta sigma weight residual 1.529 1.598 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.529 1.576 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C12 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.538 1.498 0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 8081 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.64: 182 106.64 - 113.50: 4432 113.50 - 120.36: 3089 120.36 - 127.21: 3179 127.21 - 134.07: 81 Bond angle restraints: 10963 Sorted by residual: angle pdb=" N VAL R 156 " pdb=" CA VAL R 156 " pdb=" C VAL R 156 " ideal model delta sigma weight residual 110.62 116.74 -6.12 1.02e+00 9.61e-01 3.59e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C4 P2E R 401 " pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " ideal model delta sigma weight residual 127.52 112.65 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " pdb=" C7 P2E R 401 " ideal model delta sigma weight residual 125.83 111.98 13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" N GLN A 390 " pdb=" CA GLN A 390 " pdb=" C GLN A 390 " ideal model delta sigma weight residual 111.71 116.83 -5.12 1.15e+00 7.56e-01 1.98e+01 ... (remaining 10958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4325 16.25 - 32.49: 386 32.49 - 48.74: 82 48.74 - 64.98: 17 64.98 - 81.23: 9 Dihedral angle restraints: 4819 sinusoidal: 1848 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -4.97 -81.03 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 4816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.119: 206 0.119 - 0.178: 19 0.178 - 0.238: 1 0.238 - 0.297: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C15 P2E R 401 " pdb=" C14 P2E R 401 " pdb=" C16 P2E R 401 " pdb=" O5 P2E R 401 " both_signs ideal model delta sigma weight residual False 2.23 2.52 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C8 P2E R 401 " pdb=" C12 P2E R 401 " pdb=" C7 P2E R 401 " pdb=" C9 P2E R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN A 390 " pdb=" N GLN A 390 " pdb=" C GLN A 390 " pdb=" CB GLN A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1249 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 P2E R 401 " -0.269 2.00e-02 2.50e+03 2.73e-01 7.46e+02 pdb=" C13 P2E R 401 " 0.249 2.00e-02 2.50e+03 pdb=" C14 P2E R 401 " 0.296 2.00e-02 2.50e+03 pdb=" C15 P2E R 401 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 388 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU A 388 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU A 388 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 389 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 401 " -0.028 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C5 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C6 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 P2E R 401 " -0.028 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 45 2.58 - 3.16: 6354 3.16 - 3.74: 11864 3.74 - 4.32: 17380 4.32 - 4.90: 28736 Nonbonded interactions: 64379 Sorted by model distance: nonbonded pdb=" O ILE A 56 " pdb=" N MET A 60 " model vdw 1.994 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.088 2.440 nonbonded pdb=" OG1 THR R 82 " pdb=" O HOH R 501 " model vdw 2.133 2.440 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.247 2.520 nonbonded pdb=" O GLU A 50 " pdb=" NH2 ARG A 265 " model vdw 2.276 2.520 ... (remaining 64374 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5027 2.51 5 N 1374 2.21 5 O 1477 1.98 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: 0.260 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: 2.180 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 24.440 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.004 0.079 8086 Z= 0.281 Angle : 0.712 14.865 10963 Z= 0.396 Chirality : 0.047 0.297 1252 Planarity : 0.009 0.273 1402 Dihedral : 13.588 81.229 2886 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.12 % 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: -2.13 (0.23), residues: 1002 helix: -0.55 (0.24), residues: 371 sheet: -0.79 (0.32), residues: 210 loop : -2.51 (0.24), residues: 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.928 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 1.2036 time to fit residues: 218.7771 Evaluate side-chains 124 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 0.0670 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 213 GLN A 390 GLN B 17 GLN B 32 GLN B 175 GLN B 176 GLN B 340 ASN G 5 ASN G 59 ASN N 35 ASN N 77 ASN N 82 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 8086 Z= 0.158 Angle : 0.525 10.136 10963 Z= 0.266 Chirality : 0.041 0.166 1252 Planarity : 0.004 0.053 1402 Dihedral : 4.514 42.253 1118 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 1.79 % 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: -0.76 (0.25), residues: 1002 helix: 0.92 (0.27), residues: 385 sheet: -0.32 (0.33), residues: 210 loop : -2.04 (0.26), residues: 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 153 average time/residue: 1.2616 time to fit residues: 203.7769 Evaluate side-chains 130 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.1601 time to fit residues: 1.8457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN B 32 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 8086 Z= 0.156 Angle : 0.508 9.566 10963 Z= 0.256 Chirality : 0.040 0.144 1252 Planarity : 0.004 0.054 1402 Dihedral : 4.178 25.440 1118 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 2.74 % 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: -0.17 (0.26), residues: 1002 helix: 1.40 (0.27), residues: 386 sheet: -0.06 (0.33), residues: 209 loop : -1.65 (0.27), residues: 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 0.903 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 146 average time/residue: 1.2335 time to fit residues: 190.5031 Evaluate side-chains 126 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1853 time to fit residues: 2.0173 ------------------------------------------------------------------------------- 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-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 51.7759 > 50: distance: 31 - 34: 13.871 distance: 34 - 35: 16.659 distance: 35 - 36: 12.462 distance: 35 - 38: 22.987 distance: 36 - 37: 23.624 distance: 36 - 41: 16.726 distance: 38 - 39: 13.811 distance: 38 - 40: 17.301 distance: 41 - 42: 19.198 distance: 41 - 47: 12.611 distance: 42 - 43: 13.253 distance: 42 - 45: 8.238 distance: 43 - 44: 31.270 distance: 43 - 48: 23.240 distance: 45 - 46: 22.131 distance: 46 - 47: 6.602 distance: 48 - 49: 28.236 distance: 49 - 50: 23.049 distance: 49 - 52: 8.532 distance: 50 - 51: 21.579 distance: 50 - 57: 4.873 distance: 52 - 53: 12.237 distance: 53 - 54: 13.930 distance: 54 - 55: 4.683 distance: 54 - 56: 5.566 distance: 57 - 58: 12.719 distance: 57 - 63: 9.133 distance: 58 - 59: 14.460 distance: 58 - 61: 19.747 distance: 59 - 60: 30.821 distance: 59 - 64: 10.557 distance: 61 - 62: 16.411 distance: 62 - 63: 19.714 distance: 64 - 65: 9.312 distance: 65 - 66: 8.844 distance: 66 - 67: 26.434 distance: 66 - 68: 12.664 distance: 68 - 69: 14.224 distance: 69 - 70: 29.060 distance: 69 - 72: 17.103 distance: 70 - 71: 18.481 distance: 70 - 77: 19.167 distance: 72 - 73: 14.165 distance: 73 - 74: 7.166 distance: 74 - 75: 3.526 distance: 74 - 76: 4.420 distance: 77 - 78: 11.157 distance: 78 - 79: 20.423 distance: 78 - 81: 26.172 distance: 79 - 80: 29.919 distance: 79 - 85: 30.275 distance: 81 - 82: 25.922 distance: 82 - 83: 7.831 distance: 82 - 84: 19.041 distance: 85 - 86: 26.742 distance: 85 - 91: 27.315 distance: 86 - 87: 18.216 distance: 86 - 89: 14.978 distance: 87 - 88: 28.649 distance: 87 - 92: 19.600 distance: 88 - 117: 21.330 distance: 89 - 90: 22.217 distance: 90 - 91: 15.526 distance: 92 - 93: 21.315 distance: 93 - 94: 20.246 distance: 93 - 96: 20.290 distance: 94 - 95: 18.721 distance: 94 - 103: 16.232 distance: 95 - 124: 12.524 distance: 96 - 97: 28.255 distance: 98 - 99: 6.138 distance: 103 - 104: 6.507 distance: 104 - 105: 8.052 distance: 104 - 107: 13.850 distance: 105 - 106: 20.859 distance: 105 - 110: 8.054 distance: 106 - 129: 14.395 distance: 107 - 108: 11.771 distance: 107 - 109: 10.360