Starting phenix.real_space_refine on Wed May 8 23:44:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy5_35814/05_2024/8iy5_35814.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy5_35814/05_2024/8iy5_35814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy5_35814/05_2024/8iy5_35814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy5_35814/05_2024/8iy5_35814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy5_35814/05_2024/8iy5_35814.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy5_35814/05_2024/8iy5_35814.pdb" } resolution = 2.8 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 ------------------------------------------------------------------------------- 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= 0.501 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2308 atoms to isotropic. 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 76 5.16 5 C 5847 2.51 5 N 1541 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 200": "OD1" <-> "OD2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 9176 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1764 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 316, 2465 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 302} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 316, 2465 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 302} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 2521 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 5.79, per 1000 atoms: 0.63 Number of scatterers: 9176 At special positions: 0 Unit cell: (88.312, 124.334, 139.44, 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 76 16.00 O 1712 8.00 N 1541 7.00 C 5847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 2.1 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 36.5% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.908A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.523A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 4.572A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.732A pdb=" N LYS A 280 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 281' Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.892A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.758A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.606A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 4.353A pdb=" N ALA C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.913A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.773A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 129 Processing helix chain 'R' and resid 134 through 165 Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 171 through 205 Proline residue: R 178 - end of helix removed outlier: 3.694A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 233 removed outlier: 3.861A pdb=" N THR R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 239 Processing helix chain 'R' and resid 263 through 281 removed outlier: 5.992A pdb=" N ASP R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TRP R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 Processing helix chain 'R' and resid 313 through 350 removed outlier: 3.666A pdb=" N GLN R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE R 332 " --> pdb=" O LEU R 328 " (cutoff:3.500A) Proline residue: R 338 - end of helix removed outlier: 3.678A pdb=" N TYR R 350 " --> pdb=" O LYS R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 390 removed outlier: 3.754A pdb=" N VAL R 366 " --> pdb=" O SER R 362 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 403 Processing helix chain 'L' and resid 8 through 18 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.264A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.858A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.851A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.536A 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 153 removed outlier: 5.151A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.009A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.670A 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: 6.655A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.643A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.167A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.188A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 240 through 247 445 hydrogen bonds defined for protein. 1268 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: 2.80 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2948 1.34 - 1.46: 2274 1.46 - 1.59: 4041 1.59 - 1.71: 0 1.71 - 1.83: 104 Bond restraints: 9367 Sorted by residual: bond pdb=" CA ASP B 312 " pdb=" C ASP B 312 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.58e+00 bond pdb=" C VAL E 12 " pdb=" N GLN E 13 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.47e-02 4.63e+03 2.24e+00 bond pdb=" C CYS B 114 " pdb=" N GLY B 115 " ideal model delta sigma weight residual 1.326 1.340 -0.013 1.09e-02 8.42e+03 1.50e+00 bond pdb=" CB PRO A 288 " pdb=" CG PRO A 288 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.44e+00 bond pdb=" CA VAL R 177 " pdb=" CB VAL R 177 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.16e+00 ... (remaining 9362 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.60: 148 105.60 - 112.70: 4967 112.70 - 119.80: 3085 119.80 - 126.90: 4378 126.90 - 134.00: 116 Bond angle restraints: 12694 Sorted by residual: angle pdb=" CA CYS B 103 " pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 114.40 128.17 -13.77 2.30e+00 1.89e-01 3.59e+01 angle pdb=" N GLY R 239 " pdb=" CA GLY R 239 " pdb=" C GLY R 239 " ideal model delta sigma weight residual 112.49 119.59 -7.10 1.21e+00 6.83e-01 3.45e+01 angle pdb=" N GLY B 115 " pdb=" CA GLY B 115 " pdb=" C GLY B 115 " ideal model delta sigma weight residual 111.19 117.89 -6.70 1.45e+00 4.76e-01 2.14e+01 angle pdb=" CA CYS B 114 " pdb=" CB CYS B 114 " pdb=" SG CYS B 114 " ideal model delta sigma weight residual 114.40 122.61 -8.21 2.30e+00 1.89e-01 1.27e+01 angle pdb=" C HIS E 220 " pdb=" N LEU E 221 " pdb=" CA LEU E 221 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 ... (remaining 12689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5083 17.75 - 35.50: 422 35.50 - 53.25: 66 53.25 - 71.00: 7 71.00 - 88.74: 8 Dihedral angle restraints: 5586 sinusoidal: 2166 harmonic: 3420 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 358 " pdb=" CB CYS R 358 " ideal model delta sinusoidal sigma weight residual 93.00 42.81 50.19 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual -86.00 -36.60 -49.40 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CA HIS E 220 " pdb=" C HIS E 220 " pdb=" N LEU E 221 " pdb=" CA LEU E 221 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1139 0.049 - 0.098: 247 0.098 - 0.148: 61 0.148 - 0.197: 2 0.197 - 0.246: 1 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CA CYS B 103 " pdb=" N CYS B 103 " pdb=" C CYS B 103 " pdb=" CB CYS B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA TYR E 178 " pdb=" N TYR E 178 " pdb=" C TYR E 178 " pdb=" CB TYR E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1447 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 221 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C LEU E 221 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU E 221 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU E 222 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO C 55 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 250 " -0.012 2.00e-02 2.50e+03 1.27e-02 2.82e+00 pdb=" CG PHE A 250 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 250 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 250 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 250 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 250 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 250 " 0.001 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 324 2.71 - 3.26: 9092 3.26 - 3.81: 14927 3.81 - 4.35: 18752 4.35 - 4.90: 31786 Nonbonded interactions: 74881 Sorted by model distance: nonbonded pdb=" O PHE E 32 " pdb=" NH2 ARG E 72 " model vdw 2.166 2.520 nonbonded pdb=" OD1 ASP A 350 " pdb=" ND2 ASN R 134 " model vdw 2.178 2.520 nonbonded pdb=" OD1 ASP B 290 " pdb=" NE ARG B 314 " model vdw 2.193 2.520 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.223 2.440 nonbonded pdb=" OG SER R 342 " pdb=" OD1 ASP R 368 " model vdw 2.238 2.440 ... (remaining 74876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.970 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.180 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 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 : 0.003 0.060 9367 Z= 0.188 Angle : 0.684 13.775 12694 Z= 0.395 Chirality : 0.044 0.246 1450 Planarity : 0.004 0.054 1600 Dihedral : 13.175 88.745 3357 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.88 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.34 (0.25), residues: 1160 helix: 1.59 (0.27), residues: 381 sheet: -0.66 (0.30), residues: 290 loop : -1.40 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 332 HIS 0.004 0.001 HIS E 35 PHE 0.030 0.002 PHE A 250 TYR 0.022 0.001 TYR E 178 ARG 0.009 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.935 Fit side-chains REVERT: B 76 ASP cc_start: 0.6166 (p0) cc_final: 0.5740 (p0) REVERT: C 38 MET cc_start: 0.5927 (mmm) cc_final: 0.5559 (mmt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.8858 time to fit residues: 156.5560 Evaluate side-chains 130 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 104 optimal weight: 0.0980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 256 ASN A 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9367 Z= 0.220 Angle : 0.624 8.734 12694 Z= 0.328 Chirality : 0.045 0.225 1450 Planarity : 0.004 0.044 1600 Dihedral : 5.079 27.465 1266 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.57 % Favored : 95.17 % Rotamer: Outliers : 2.48 % Allowed : 10.03 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.22 (0.25), residues: 1160 helix: 1.50 (0.27), residues: 391 sheet: -0.58 (0.30), residues: 283 loop : -1.22 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 332 HIS 0.006 0.002 HIS B 62 PHE 0.028 0.002 PHE R 112 TYR 0.016 0.002 TYR E 178 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 ARG cc_start: 0.8181 (ttt180) cc_final: 0.7869 (ttt180) outliers start: 25 outliers final: 14 residues processed: 146 average time/residue: 0.8098 time to fit residues: 127.6482 Evaluate side-chains 140 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.0870 chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: