Starting phenix.real_space_refine on Sat Aug 3 01:34:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/08_2024/8uno_42411.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/08_2024/8uno_42411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/08_2024/8uno_42411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/08_2024/8uno_42411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/08_2024/8uno_42411.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uno_42411/08_2024/8uno_42411.cif" } resolution = 3.3 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= 0.023 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 37 5.16 5 C 4186 2.51 5 N 1117 2.21 5 O 1146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 226": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6489 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1669 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 5 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Conformer: "B" Number of residues, atoms: 223, 1657 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 5 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 bond proxies already assigned to first conformer: 1674 Chain: "B" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2335 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 154 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 349 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2089 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 4.96, per 1000 atoms: 0.76 Number of scatterers: 6489 At special positions: 0 Unit cell: (82.4315, 131.023, 95.447, 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 37 16.00 P 3 15.00 O 1146 8.00 N 1117 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.4 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 49.9% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 14 through 40 removed outlier: 3.683A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.764A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.797A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.522A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.806A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.688A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.552A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.873A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 7 through 11' Processing helix chain 'B' and resid 11 through 26 removed outlier: 4.107A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.513A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.823A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.650A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 33 through 61 removed outlier: 3.782A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.402A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.829A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.810A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.520A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 4.050A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.825A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 3.715A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.716A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.728A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 removed outlier: 3.709A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.610A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.630A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.830A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.084A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.049A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.546A 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 151 removed outlier: 3.619A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.784A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.906A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.673A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1017 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: 1.68 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1617 1.33 - 1.45: 1351 1.45 - 1.57: 3607 1.57 - 1.69: 5 1.69 - 1.81: 51 Bond restraints: 6631 Sorted by residual: bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.472 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CA ASN A 254 " pdb=" C ASN A 254 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.24e-02 6.50e+03 1.48e+01 bond pdb=" CA VAL R 39 " pdb=" C VAL R 39 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.22e-02 6.72e+03 1.39e+01 bond pdb=" C4 GTP A 401 " pdb=" C5 GTP A 401 " ideal model delta sigma weight residual 1.390 1.459 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA GLU B 12 " pdb=" C GLU B 12 " ideal model delta sigma weight residual 1.522 1.477 0.045 1.41e-02 5.03e+03 1.03e+01 ... (remaining 6626 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.51: 210 107.51 - 114.61: 3897 114.61 - 121.71: 3529 121.71 - 128.81: 1387 128.81 - 135.91: 59 Bond angle restraints: 9082 Sorted by residual: angle pdb=" N GLU B 12 " pdb=" CA GLU B 12 " pdb=" C GLU B 12 " ideal model delta sigma weight residual 112.38 102.27 10.11 1.22e+00 6.72e-01 6.86e+01 angle pdb=" N LEU G 19 " pdb=" CA LEU G 19 " pdb=" C LEU G 19 " ideal model delta sigma weight residual 111.28 102.85 8.43 1.09e+00 8.42e-01 5.98e+01 angle pdb=" N ASN B 35 " pdb=" CA ASN B 35 " pdb=" C ASN B 35 " ideal model delta sigma weight residual 111.28 117.24 -5.96 1.09e+00 8.42e-01 2.99e+01 angle pdb=" N ASN B 36 " pdb=" CA ASN B 36 " pdb=" C ASN B 36 " ideal model delta sigma weight residual 111.28 116.68 -5.40 1.09e+00 8.42e-01 2.46e+01 angle pdb=" N GLN B 9 " pdb=" CA GLN B 9 " pdb=" C GLN B 9 " ideal model delta sigma weight residual 112.38 106.94 5.44 1.22e+00 6.72e-01 1.99e+01 ... (remaining 9077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 3629 22.87 - 45.75: 163 45.75 - 68.62: 8 68.62 - 91.50: 7 91.50 - 114.37: 3 Dihedral angle restraints: 3810 sinusoidal: 1196 harmonic: 2614 Sorted by residual: dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual -56.21 -170.58 114.37 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 2.67 101.92 1 2.00e+01 2.50e-03 2.90e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 165.10 -95.83 1 2.00e+01 2.50e-03 2.64e+01 ... (remaining 3807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 784 0.039 - 0.078: 219 0.078 - 0.118: 80 0.118 - 0.157: 10 0.157 - 0.196: 3 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CA ALA B 11 " pdb=" N ALA B 11 " pdb=" C ALA B 11 " pdb=" CB ALA B 11 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA ALA B 305 " pdb=" N ALA B 305 " pdb=" C ALA B 305 " pdb=" CB ALA B 305 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 1093 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.050 5.00e-02 4.00e+02 7.73e-02 9.57e+00 pdb=" N PRO B 39 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO G 49 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 253 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C TYR A 253 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR A 253 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN A 254 " -0.016 2.00e-02 2.50e+03 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1229 2.77 - 3.30: 6029 3.30 - 3.83: 9956 3.83 - 4.37: 10994 4.37 - 4.90: 20206 Nonbonded interactions: 48414 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.236 3.040 nonbonded pdb=" O SER R 111 " pdb=" OG SER R 165 " model vdw 2.333 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.347 3.040 nonbonded pdb=" N GLU A 50 " pdb=" O2G GTP A 401 " model vdw 2.368 3.120 nonbonded pdb=" N CYS A 365 " pdb=" OD2 ASP A 368 " model vdw 2.387 3.120 ... (remaining 48409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 3.260 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.560 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 0.082 6631 Z= 0.330 Angle : 0.669 10.589 9082 Z= 0.406 Chirality : 0.042 0.196 1096 Planarity : 0.005 0.077 1132 Dihedral : 13.445 114.370 2110 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.17 % Allowed : 0.69 % Favored : 99.13 % 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: 1.15 (0.29), residues: 875 helix: 2.00 (0.28), residues: 387 sheet: 0.65 (0.42), residues: 173 loop : -0.72 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 211 HIS 0.006 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.023 0.001 TYR A 253 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.704 Fit side-chains REVERT: G 48 ASP cc_start: 0.7982 (p0) cc_final: 0.7777 (p0) REVERT: R 103 ASN cc_start: 0.6069 (m-40) cc_final: 0.5818 (m-40) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1871 time to fit residues: 27.5155 Evaluate side-chains 91 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6631 Z= 0.320 Angle : 0.559 7.259 9082 Z= 0.301 Chirality : 0.043 0.157 1096 Planarity : 0.004 0.066 1132 Dihedral : 8.497 121.847 977 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.21 % Allowed : 9.86 % Favored : 88.93 % 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: 0.98 (0.29), residues: 875 helix: 1.88 (0.27), residues: 391 sheet: 0.38 (0.39), residues: 177 loop : -0.77 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.007 0.002 HIS B 183 PHE 0.015 0.002 PHE B 199 TYR 0.012 0.001 TYR A 311 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.695 Fit side-chains REVERT: G 27 ARG cc_start: 0.8339 (mtt90) cc_final: 0.8138 (mtt90) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.2347 time to fit residues: 29.1095 Evaluate side-chains 87 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain R residue 190 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 0.0370 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6631 Z= 0.152 Angle : 0.470 6.320 9082 Z= 0.251 Chirality : 0.041 0.173 1096 Planarity : 0.004 0.073 1132 Dihedral : 8.204 126.433 977 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.38 % Allowed : 12.28 % Favored : 86.33 % 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: 1.29 (0.30), residues: 875 helix: 2.27 (0.28), residues: 386 sheet: 0.28 (0.39), residues: 178 loop : -0.59 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.001 PHE B 199 TYR 0.010 0.001 TYR B 124 ARG 0.001 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.706 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 0.1973 time to fit residues: 24.3091 Evaluate side-chains 83 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 30.0000 chunk 70 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6631 Z= 0.163 Angle : 0.469 6.200 9082 Z= 0.250 Chirality : 0.040 0.179 1096 Planarity : 0.004 0.076 1132 Dihedral : 8.024 129.067 977 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.90 % Allowed : 13.32 % Favored : 84.78 % 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: 1.35 (0.30), residues: 875 helix: 2.36 (0.28), residues: 386 sheet: 0.26 (0.39), residues: 178 loop : -0.58 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE B 199 TYR 0.008 0.001 TYR B 124 ARG 0.001 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.690 Fit side-chains REVERT: B 59 TYR cc_start: 0.8324 (m-80) cc_final: 0.7947 (m-80) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.1913 time to fit residues: 23.0812 Evaluate side-chains 89 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 237 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6631 Z= 0.143 Angle : 0.454 6.253 9082 Z= 0.242 Chirality : 0.040 0.188 1096 Planarity : 0.004 0.077 1132 Dihedral : 7.890 131.268 977 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.73 % Allowed : 13.84 % Favored : 84.43 % 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: 1.44 (0.30), residues: 875 helix: 2.44 (0.28), residues: 386 sheet: 0.25 (0.40), residues: 178 loop : -0.51 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.007 0.001 TYR B 124 ARG 0.001 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.731 Fit side-chains REVERT: B 59 TYR cc_start: 0.8301 (m-80) cc_final: 0.7924 (m-80) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.1948 time to fit residues: 24.1269 Evaluate side-chains 86 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 269 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 56.3361 > 50: distance: 44 - 134: 19.869 distance: 53 - 124: 16.981 distance: 56 - 121: 9.917 distance: 60 - 69: 13.535 distance: 69 - 70: 30.336 distance: 70 - 71: 13.102 distance: 70 - 73: 15.168 distance: 71 - 72: 13.006 distance: 71 - 75: 43.909 distance: 73 - 74: 13.296 distance: 75 - 76: 20.218 distance: 76 - 77: 24.217 distance: 76 - 79: 32.828 distance: 77 - 78: 21.102 distance: 77 - 84: 15.226 distance: 79 - 80: 28.872 distance: 80 - 81: 12.303 distance: 81 - 82: 35.024 distance: 82 - 83: 14.208 distance: 84 - 85: 9.159 distance: 85 - 86: 27.403 distance: 85 - 88: 24.904 distance: 86 - 87: 16.108 distance: 86 - 90: 36.756 distance: 88 - 89: 39.201 distance: 90 - 91: 12.235 distance: 91 - 92: 26.450 distance: 92 - 93: 20.137 distance: 92 - 94: 16.098 distance: 94 - 95: 28.364 distance: 95 - 96: 11.747 distance: 95 - 98: 5.454 distance: 96 - 97: 17.223 distance: 96 - 105: 9.777 distance: 98 - 99: 9.947 distance: 99 - 100: 15.137 distance: 100 - 101: 16.509 distance: 102 - 103: 10.401 distance: 102 - 104: 3.292 distance: 105 - 106: 20.183 distance: 106 - 107: 32.778 distance: 106 - 109: 29.975 distance: 107 - 108: 21.556 distance: 107 - 113: 12.839 distance: 109 - 110: 14.978 distance: 110 - 112: 20.486 distance: 113 - 114: 15.510 distance: 114 - 115: 4.480 distance: 114 - 117: 18.338 distance: 115 - 116: 4.936 distance: 115 - 121: 4.925 distance: 116 - 171: 8.003 distance: 117 - 118: 6.584 distance: 118 - 119: 18.032 distance: 118 - 120: 20.248 distance: 122 - 123: 17.583 distance: 122 - 125: 6.886 distance: 123 - 124: 8.228 distance: 123 - 129: 11.073 distance: 125 - 126: 20.375 distance: 126 - 127: 29.915 distance: 126 - 128: 6.197 distance: 129 - 130: 17.080 distance: 129 - 160: 6.219 distance: 130 - 131: 21.719 distance: 130 - 133: 8.264 distance: 131 - 132: 27.385 distance: 131 - 134: 21.617 distance: 132 - 157: 8.579 distance: 134 - 135: 26.003 distance: 135 - 136: 54.350 distance: 136 - 137: 40.946 distance: 136 - 138: 28.327