Starting phenix.real_space_refine on Tue Apr 29 09:01:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsp_36626/04_2025/8jsp_36626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsp_36626/04_2025/8jsp_36626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jsp_36626/04_2025/8jsp_36626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsp_36626/04_2025/8jsp_36626.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsp_36626/04_2025/8jsp_36626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsp_36626/04_2025/8jsp_36626.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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 63 5.16 5 C 5480 2.51 5 N 1470 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8599 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1743 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2516 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "E" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1717 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2264 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 1 Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.59 Number of scatterers: 8599 At special positions: 0 Unit cell: (103.96, 115.92, 129.72, 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 63 16.00 O 1586 8.00 N 1470 7.00 C 5480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.07 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.07 Conformation dependent library (CDL) restraints added in 930.0 milliseconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 39.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.509A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.503A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.055A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.960A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.517A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 removed outlier: 3.523A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.847A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.774A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.961A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.806A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 63 removed outlier: 3.686A pdb=" N VAL R 58 " --> pdb=" O ASN R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 99 Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 105 through 123 Processing helix chain 'R' and resid 124 through 140 removed outlier: 4.227A pdb=" N CYS R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP R 140 " --> pdb=" O TRP R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 removed outlier: 3.551A pdb=" N TYR R 144 " --> pdb=" O ASP R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 174 removed outlier: 3.937A pdb=" N ALA R 154 " --> pdb=" O PRO R 150 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 192 through 228 removed outlier: 4.060A pdb=" N THR R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Proline residue: R 207 - end of helix removed outlier: 3.661A pdb=" N ILE R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 357 removed outlier: 3.741A pdb=" N THR R 343 " --> pdb=" O ARG R 339 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL R 344 " --> pdb=" O GLU R 340 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 368 Processing helix chain 'R' and resid 369 through 373 removed outlier: 4.324A pdb=" N GLU R 372 " --> pdb=" O PRO R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 401 removed outlier: 3.785A pdb=" N ILE R 384 " --> pdb=" O LEU R 380 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix removed outlier: 3.692A pdb=" N TYR R 400 " --> pdb=" O ASN R 396 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 200 removed outlier: 4.142A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.556A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.811A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 112 removed outlier: 4.076A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.546A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.831A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.836A 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: 6.830A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.896A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.679A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 83 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE E 80 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 4.008A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E 206 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.736A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 3.702A pdb=" N LEU E 178 " --> pdb=" O GLN E 186 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E 188 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1065 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: 2.48 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1561 1.32 - 1.45: 2279 1.45 - 1.57: 4849 1.57 - 1.69: 0 1.69 - 1.82: 90 Bond restraints: 8779 Sorted by residual: bond pdb=" C VAL R 89 " pdb=" O VAL R 89 " ideal model delta sigma weight residual 1.236 1.279 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.16e+01 bond pdb=" N CYS B 149 " pdb=" CA CYS B 149 " ideal model delta sigma weight residual 1.462 1.500 -0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" C VAL R 85 " pdb=" O VAL R 85 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.12e-02 7.97e+03 9.49e+00 bond pdb=" N CYS R 120 " pdb=" CA CYS R 120 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.33e-02 5.65e+03 9.11e+00 ... (remaining 8774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11470 1.93 - 3.87: 356 3.87 - 5.80: 56 5.80 - 7.73: 8 7.73 - 9.67: 3 Bond angle restraints: 11893 Sorted by residual: angle pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta sigma weight residual 122.89 113.22 9.67 1.12e+00 7.97e-01 7.45e+01 angle pdb=" N VAL R 85 " pdb=" CA VAL R 85 " pdb=" CB VAL R 85 " ideal model delta sigma weight residual 110.62 116.10 -5.48 1.05e+00 9.07e-01 2.72e+01 angle pdb=" C CYS B 121 " pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " ideal model delta sigma weight residual 111.23 118.17 -6.94 1.42e+00 4.96e-01 2.39e+01 angle pdb=" CA VAL R 85 " pdb=" C VAL R 85 " pdb=" O VAL R 85 " ideal model delta sigma weight residual 121.41 116.94 4.47 1.04e+00 9.25e-01 1.85e+01 angle pdb=" N MET R 84 " pdb=" CA MET R 84 " pdb=" C MET R 84 " ideal model delta sigma weight residual 111.02 105.89 5.13 1.22e+00 6.72e-01 1.77e+01 ... (remaining 11888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4688 17.31 - 34.62: 435 34.62 - 51.93: 78 51.93 - 69.24: 13 69.24 - 86.55: 9 Dihedral angle restraints: 5223 sinusoidal: 2031 harmonic: 3192 Sorted by residual: dihedral pdb=" CA LEU B 79 " pdb=" C LEU B 79 " pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TYR E 235 " pdb=" C TYR E 235 " pdb=" N PRO E 236 " pdb=" CA PRO E 236 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 923 0.045 - 0.089: 318 0.089 - 0.134: 94 0.134 - 0.179: 16 0.179 - 0.223: 2 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CB THR A 327 " pdb=" CA THR A 327 " pdb=" OG1 THR A 327 " pdb=" CG2 THR A 327 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL R 85 " pdb=" CA VAL R 85 " pdb=" CG1 VAL R 85 " pdb=" CG2 VAL R 85 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1350 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 120 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C ILE B 120 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 120 " 0.018 2.00e-02 2.50e+03 pdb=" N CYS B 121 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 407 " 0.022 2.00e-02 2.50e+03 1.86e-02 6.03e+00 pdb=" CG PHE R 407 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE R 407 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 407 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 407 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 407 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 407 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP R 140 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO R 141 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 141 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 141 " 0.032 5.00e-02 4.00e+02 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 985 2.74 - 3.28: 8673 3.28 - 3.82: 13698 3.82 - 4.36: 15583 4.36 - 4.90: 27107 Nonbonded interactions: 66046 Sorted by model distance: nonbonded pdb=" NE1 TRP E 47 " pdb=" O ALA E 49 " model vdw 2.204 3.120 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.211 3.040 nonbonded pdb=" O ARG E 98 " pdb=" OG SER E 99 " model vdw 2.234 3.040 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.237 3.120 nonbonded pdb=" O ASP E 90 " pdb=" OH TYR E 94 " model vdw 2.239 3.040 ... (remaining 66041 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.090 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.060 Find NCS groups from input model: 0.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8783 Z= 0.291 Angle : 0.794 9.666 11901 Z= 0.461 Chirality : 0.049 0.223 1353 Planarity : 0.005 0.058 1497 Dihedral : 14.057 86.552 3153 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.86 % Allowed : 0.86 % Favored : 98.27 % 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: -0.89 (0.25), residues: 1084 helix: 0.72 (0.26), residues: 383 sheet: -0.93 (0.34), residues: 239 loop : -1.47 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 82 HIS 0.008 0.002 HIS B 91 PHE 0.042 0.003 PHE R 407 TYR 0.026 0.003 TYR R 96 ARG 0.004 0.001 ARG E 191 Details of bonding type rmsd hydrogen bonds : bond 0.20229 ( 373) hydrogen bonds : angle 7.46001 ( 1065) SS BOND : bond 0.01735 ( 4) SS BOND : angle 0.48708 ( 8) covalent geometry : bond 0.00605 ( 8779) covalent geometry : angle 0.79441 (11893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.939 Fit side-chains REVERT: A 346 ASN cc_start: 0.7768 (m110) cc_final: 0.7446 (m-40) REVERT: E 93 MET cc_start: 0.7738 (mpp) cc_final: 0.6880 (mpp) REVERT: R 330 GLU cc_start: 0.8616 (tp30) cc_final: 0.8403 (tp30) REVERT: R 337 LEU cc_start: 0.8831 (mm) cc_final: 0.8514 (mm) outliers start: 8 outliers final: 3 residues processed: 172 average time/residue: 0.1944 time to fit residues: 46.5879 Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 230 ASN E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.217520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.174471 restraints weight = 10943.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.175889 restraints weight = 7555.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.179116 restraints weight = 6359.149| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8783 Z= 0.129 Angle : 0.617 7.209 11901 Z= 0.325 Chirality : 0.043 0.181 1353 Planarity : 0.004 0.041 1497 Dihedral : 5.601 88.325 1212 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.37 % Allowed : 9.28 % Favored : 88.35 % 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: -0.49 (0.26), residues: 1084 helix: 1.17 (0.27), residues: 387 sheet: -0.81 (0.33), residues: 242 loop : -1.33 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.004 0.001 HIS E 232 PHE 0.015 0.001 PHE B 292 TYR 0.030 0.002 TYR E 235 ARG 0.004 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 373) hydrogen bonds : angle 5.10621 ( 1065) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.65561 ( 8) covalent geometry : bond 0.00281 ( 8779) covalent geometry : angle 0.61665 (11893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.119 Fit side-chains REVERT: A 346 ASN cc_start: 0.7552 (m110) cc_final: 0.7235 (m110) REVERT: B 262 MET cc_start: 0.6722 (tpt) cc_final: 0.6187 (tpp) REVERT: B 266 HIS cc_start: 0.7396 (t-90) cc_final: 0.7190 (t-90) REVERT: E 230 MET cc_start: 0.5166 (ppp) cc_final: 0.4587 (ttp) REVERT: E 231 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6707 (pp30) REVERT: R 113 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7712 (mm) REVERT: R 333 ARG cc_start: 0.8555 (ptp-170) cc_final: 0.8243 (ptp-170) REVERT: R 335 MET cc_start: 0.7477 (ttp) cc_final: 0.7190 (ttm) outliers start: 22 outliers final: 16 residues processed: 162 average time/residue: 0.1938 time to fit residues: 43.8169 Evaluate side-chains 146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 344 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.213900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.170909 restraints weight = 11128.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.172208 restraints weight = 7801.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175183 restraints weight = 6499.189| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8783 Z= 0.143 Angle : 0.604 7.667 11901 Z= 0.320 Chirality : 0.043 0.176 1353 Planarity : 0.004 0.048 1497 Dihedral : 5.183 85.841 1211 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.70 % Allowed : 13.05 % Favored : 84.25 % 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: -0.45 (0.26), residues: 1084 helix: 1.28 (0.27), residues: 387 sheet: -0.86 (0.32), residues: 249 loop : -1.33 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.014 0.001 PHE R 362 TYR 0.029 0.002 TYR A 230 ARG 0.003 0.000 ARG E 180 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 373) hydrogen bonds : angle 4.87748 ( 1065) SS BOND : bond 0.00906 ( 4) SS BOND : angle 0.55500 ( 8) covalent geometry : bond 0.00333 ( 8779) covalent geometry : angle 0.60355 (11893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.946 Fit side-chains REVERT: A 47 ASN cc_start: 0.8406 (p0) cc_final: 0.8110 (p0) REVERT: A 346 ASN cc_start: 0.7652 (m110) cc_final: 0.7229 (m110) REVERT: B 266 HIS cc_start: 0.7519 (t-90) cc_final: 0.7192 (t-170) REVERT: R 113 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7745 (mm) REVERT: R 333 ARG cc_start: 0.8538 (ptp-170) cc_final: 0.8337 (ptp-170) outliers start: 25 outliers final: 21 residues processed: 154 average time/residue: 0.2030 time to fit residues: 43.4746 Evaluate side-chains 153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 0.0570 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 103 optimal weight: 0.0170 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS E 231 GLN R 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.220564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.178791 restraints weight = 11087.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.180438 restraints weight = 7565.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.183486 restraints weight = 6226.912| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8783 Z= 0.106 Angle : 0.557 6.732 11901 Z= 0.293 Chirality : 0.041 0.141 1353 Planarity : 0.003 0.044 1497 Dihedral : 4.983 88.907 1209 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.48 % Allowed : 15.97 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.22 (0.26), residues: 1084 helix: 1.48 (0.27), residues: 387 sheet: -0.73 (0.32), residues: 255 loop : -1.21 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.008 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.032 0.001 TYR E 235 ARG 0.002 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 373) hydrogen bonds : angle 4.56095 ( 1065) SS BOND : bond 0.00541 ( 4) SS BOND : angle 0.30405 ( 8) covalent geometry : bond 0.00227 ( 8779) covalent geometry : angle 0.55712 (11893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7628 (m110) cc_final: 0.7194 (m110) REVERT: B 120 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6305 (mt) REVERT: B 266 HIS cc_start: 0.7423 (t-90) cc_final: 0.7215 (t70) REVERT: E 228 TYR cc_start: 0.5805 (m-80) cc_final: 0.5461 (m-80) REVERT: E 230 MET cc_start: 0.5058 (ppp) cc_final: 0.4660 (ttp) REVERT: E 231 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6730 (pp30) REVERT: G 58 GLU cc_start: 0.8177 (pm20) cc_final: 0.7931 (pm20) REVERT: R 333 ARG cc_start: 0.8541 (ptp-170) cc_final: 0.8318 (ptp-170) REVERT: R 334 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7977 (mtmm) outliers start: 23 outliers final: 16 residues processed: 154 average time/residue: 0.2126 time to fit residues: 44.7134 Evaluate side-chains 152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 330 GLU Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.220167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.178461 restraints weight = 11071.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.180179 restraints weight = 7522.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.183045 restraints weight = 6222.094| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8783 Z= 0.108 Angle : 0.557 7.068 11901 Z= 0.291 Chirality : 0.041 0.142 1353 Planarity : 0.003 0.044 1497 Dihedral : 4.890 89.552 1207 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.02 % Allowed : 15.97 % Favored : 81.01 % 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: 1084 helix: 1.48 (0.27), residues: 388 sheet: -0.64 (0.31), residues: 266 loop : -1.20 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS E 232 PHE 0.012 0.001 PHE E 68 TYR 0.032 0.001 TYR E 235 ARG 0.002 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 373) hydrogen bonds : angle 4.42877 ( 1065) SS BOND : bond 0.00603 ( 4) SS BOND : angle 0.26947 ( 8) covalent geometry : bond 0.00239 ( 8779) covalent geometry : angle 0.55748 (11893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7590 (m110) cc_final: 0.7132 (m110) REVERT: B 266 HIS cc_start: 0.7441 (t-90) cc_final: 0.7182 (t70) REVERT: E 228 TYR cc_start: 0.5824 (m-80) cc_final: 0.5527 (m-80) REVERT: E 230 MET cc_start: 0.5161 (ppp) cc_final: 0.4773 (ttp) REVERT: R 65 ARG cc_start: 0.7216 (ttp-110) cc_final: 0.6729 (tpt90) REVERT: R 333 ARG cc_start: 0.8519 (ptp-170) cc_final: 0.8298 (ptp-170) REVERT: R 334 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7980 (mtmm) outliers start: 28 outliers final: 21 residues processed: 155 average time/residue: 0.2463 time to fit residues: 53.0981 Evaluate side-chains 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 330 GLU Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 414 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6462 > 50: distance: 28 - 48: 23.925 distance: 32 - 53: 36.676 distance: 38 - 61: 37.482 distance: 43 - 48: 24.631 distance: 44 - 69: 32.128 distance: 48 - 49: 42.600 distance: 49 - 50: 40.459 distance: 49 - 52: 30.873 distance: 50 - 51: 58.596 distance: 51 - 76: 43.752 distance: 53 - 54: 13.905 distance: 54 - 55: 26.886 distance: 54 - 57: 37.721 distance: 55 - 56: 67.130 distance: 55 - 61: 3.704 distance: 56 - 84: 55.548 distance: 57 - 58: 21.309 distance: 58 - 59: 10.767 distance: 58 - 60: 18.412 distance: 61 - 62: 7.144 distance: 62 - 63: 41.568 distance: 62 - 65: 65.072 distance: 63 - 64: 6.574 distance: 63 - 69: 27.857 distance: 64 - 90: 49.602 distance: 65 - 66: 24.306 distance: 66 - 67: 35.098 distance: 66 - 68: 26.478 distance: 69 - 70: 27.023 distance: 70 - 71: 46.560 distance: 70 - 73: 13.127 distance: 71 - 72: 10.981 distance: 71 - 76: 39.038 distance: 72 - 96: 10.455 distance: 73 - 74: 43.676 distance: 73 - 75: 46.438 distance: 76 - 77: 24.038 distance: 77 - 78: 41.603 distance: 77 - 80: 24.107 distance: 78 - 79: 41.582 distance: 78 - 84: 35.794 distance: 79 - 103: 42.073 distance: 80 - 81: 33.439 distance: 81 - 82: 52.998 distance: 81 - 83: 45.213 distance: 84 - 85: 26.009 distance: 85 - 86: 32.592 distance: 85 - 88: 25.914 distance: 86 - 87: 36.708 distance: 86 - 90: 21.248 distance: 87 - 109: 29.512 distance: 88 - 89: 42.834 distance: 90 - 91: 5.737 distance: 91 - 92: 40.126 distance: 91 - 94: 15.531 distance: 92 - 93: 47.781 distance: 92 - 96: 29.284 distance: 94 - 95: 39.368 distance: 96 - 97: 36.981 distance: 97 - 98: 23.456 distance: 97 - 100: 57.754 distance: 98 - 99: 18.670 distance: 98 - 103: 41.106 distance: 100 - 101: 54.008 distance: 100 - 102: 58.393 distance: 103 - 104: 15.440 distance: 104 - 105: 6.040 distance: 104 - 107: 6.938 distance: 105 - 106: 42.175 distance: 105 - 109: 27.450 distance: 107 - 108: 53.841 distance: 109 - 110: 52.333 distance: 110 - 111: 21.160 distance: 110 - 113: 43.657 distance: 111 - 112: 24.918 distance: 111 - 115: 29.280 distance: 113 - 114: 29.493