Starting phenix.real_space_refine on Thu Feb 13 15:47:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w2z_32268/02_2025/7w2z_32268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w2z_32268/02_2025/7w2z_32268.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/cci-nas-00/data/ceres_data/7w2z_32268/02_2025/7w2z_32268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w2z_32268/02_2025/7w2z_32268.map" model { file = "/net/cci-nas-00/data/ceres_data/7w2z_32268/02_2025/7w2z_32268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w2z_32268/02_2025/7w2z_32268.cif" } 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 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= 0.008 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 61 5.16 5 C 5812 2.51 5 N 1544 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1691 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 2 Chain: "R" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2421 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "L" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 131 Unusual residues: {'K4Q': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 11, None: 1} Not linked: pdbres="K4Q L 3 " pdbres="PHE L 4 " Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.91, per 1000 atoms: 0.54 Number of scatterers: 9080 At special positions: 0 Unit cell: (109.512, 119.652, 126.75, 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 61 16.00 O 1663 8.00 N 1544 7.00 C 5812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 36.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.554A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.320A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.865A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.050A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.524A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 71 removed outlier: 3.947A pdb=" N ALA R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL R 56 " --> pdb=" O ALA R 52 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA R 59 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET R 65 " --> pdb=" O ASN R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 75 removed outlier: 3.586A pdb=" N ARG R 75 " --> pdb=" O ARG R 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 72 through 75' Processing helix chain 'R' and resid 76 through 95 removed outlier: 3.937A pdb=" N PHE R 93 " --> pdb=" O ASP R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 105 removed outlier: 3.510A pdb=" N ASP R 99 " --> pdb=" O CYS R 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU R 100 " --> pdb=" O MET R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 147 removed outlier: 3.734A pdb=" N LEU R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 145 " --> pdb=" O ARG R 141 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE R 147 " --> pdb=" O PHE R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 175 removed outlier: 3.632A pdb=" N PHE R 165 " --> pdb=" O LYS R 161 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 181 Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 208 through 218 removed outlier: 3.673A pdb=" N TRP R 215 " --> pdb=" O THR R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 240 removed outlier: 3.577A pdb=" N LEU R 223 " --> pdb=" O ILE R 219 " (cutoff:3.500A) Proline residue: R 224 - end of helix removed outlier: 3.592A pdb=" N CYS R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL R 230 " --> pdb=" O PHE R 226 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER R 233 " --> pdb=" O THR R 229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG R 237 " --> pdb=" O SER R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 281 removed outlier: 3.596A pdb=" N VAL R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 281 through 289 Processing helix chain 'R' and resid 299 through 304 removed outlier: 3.633A pdb=" N TYR R 303 " --> pdb=" O GLN R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 315 removed outlier: 3.677A pdb=" N VAL R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 323 removed outlier: 3.907A pdb=" N TYR R 323 " --> pdb=" O ASN R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 339 removed outlier: 3.547A pdb=" N ARG R 331 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 332 " --> pdb=" O LYS R 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 22 removed outlier: 4.085A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.542A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.506A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.972A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.725A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.595A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'L' and resid 8 through 14 removed outlier: 3.881A pdb=" N VAL L 12 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 9.069A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 182 through 185 removed outlier: 3.647A pdb=" N ARG R 199 " --> pdb=" O GLY R 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.811A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.298A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.566A pdb=" N VAL S 135 " --> pdb=" O LYS S 232 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.489A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.841A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.817A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.767A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.945A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.683A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.455A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1104 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: 2.44 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 2 1.21 - 1.37: 3077 1.37 - 1.52: 3750 1.52 - 1.67: 2359 1.67 - 1.82: 86 Bond restraints: 9274 Sorted by residual: bond pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " ideal model delta sigma weight residual 1.335 1.062 0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C08 K4Q L 3 " pdb=" O09 K4Q L 3 " ideal model delta sigma weight residual 1.204 1.404 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" CB VAL B 71 " pdb=" CG2 VAL B 71 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.24e+01 bond pdb=" C VAL S 12 " pdb=" N GLN S 13 " ideal model delta sigma weight residual 1.329 1.384 -0.055 1.60e-02 3.91e+03 1.19e+01 bond pdb=" C MET R 96 " pdb=" N PRO R 97 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.36e-02 5.41e+03 9.51e+00 ... (remaining 9269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.82: 12551 6.82 - 13.64: 15 13.64 - 20.46: 2 20.46 - 27.29: 0 27.29 - 34.11: 2 Bond angle restraints: 12570 Sorted by residual: angle pdb=" C07 K4Q L 3 " pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " ideal model delta sigma weight residual 118.23 84.12 34.11 3.00e+00 1.11e-01 1.29e+02 angle pdb=" O09 K4Q L 3 " pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " ideal model delta sigma weight residual 117.69 151.08 -33.39 3.00e+00 1.11e-01 1.24e+02 angle pdb=" N VAL R 212 " pdb=" CA VAL R 212 " pdb=" C VAL R 212 " ideal model delta sigma weight residual 111.00 103.44 7.56 1.09e+00 8.42e-01 4.81e+01 angle pdb=" N LYS R 117 " pdb=" CA LYS R 117 " pdb=" C LYS R 117 " ideal model delta sigma weight residual 111.69 104.40 7.29 1.23e+00 6.61e-01 3.51e+01 angle pdb=" N ASN S 182 " pdb=" CA ASN S 182 " pdb=" C ASN S 182 " ideal model delta sigma weight residual 109.15 117.61 -8.46 1.44e+00 4.82e-01 3.45e+01 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.02: 5455 33.02 - 66.05: 127 66.05 - 99.07: 11 99.07 - 132.09: 1 132.09 - 165.11: 2 Dihedral angle restraints: 5596 sinusoidal: 2259 harmonic: 3337 Sorted by residual: dihedral pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N TYR A 354 " pdb=" CA TYR A 354 " ideal model delta harmonic sigma weight residual -180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" C11 K4Q L 3 " pdb=" C08 K4Q L 3 " pdb=" O10 K4Q L 3 " pdb=" O09 K4Q L 3 " ideal model delta sinusoidal sigma weight residual 179.48 14.37 165.11 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C04 K4Q L 3 " pdb=" C05 K4Q L 3 " pdb=" C06 K4Q L 3 " pdb=" C07 K4Q L 3 " ideal model delta sinusoidal sigma weight residual 182.71 25.83 156.88 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 5593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1285 0.097 - 0.194: 130 0.194 - 0.290: 17 0.290 - 0.387: 2 0.387 - 0.484: 1 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA MET S 180 " pdb=" N MET S 180 " pdb=" C MET S 180 " pdb=" CB MET S 180 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CA LYS A 46 " pdb=" N LYS A 46 " pdb=" C LYS A 46 " pdb=" CB LYS A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ARG S 179 " pdb=" N ARG S 179 " pdb=" C ARG S 179 " pdb=" CB ARG S 179 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 1432 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 K4Q L 3 " 0.018 2.00e-02 2.50e+03 1.03e-01 1.07e+02 pdb=" C08 K4Q L 3 " -0.173 2.00e-02 2.50e+03 pdb=" O09 K4Q L 3 " 0.069 2.00e-02 2.50e+03 pdb=" O10 K4Q L 3 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG R 107 " -0.100 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO R 108 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO R 108 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO R 108 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 277 " 0.050 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO R 278 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO R 278 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 278 " 0.042 5.00e-02 4.00e+02 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 107 2.64 - 3.21: 7511 3.21 - 3.77: 13404 3.77 - 4.34: 19629 4.34 - 4.90: 32621 Nonbonded interactions: 73272 Sorted by model distance: nonbonded pdb=" O ASN A 43 " pdb=" ND2 ASN A 43 " model vdw 2.078 3.120 nonbonded pdb=" OD2 ASP R 99 " pdb=" OH TYR R 313 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU R 197 " pdb=" OG SER L 6 " model vdw 2.258 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.290 3.040 ... (remaining 73267 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 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: 0.380 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.350 Find NCS groups from input model: 0.110 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.009 0.273 9274 Z= 0.637 Angle : 1.133 34.107 12570 Z= 0.608 Chirality : 0.064 0.484 1435 Planarity : 0.009 0.150 1577 Dihedral : 14.810 165.115 3431 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 0.82 % Allowed : 6.53 % Favored : 92.65 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % 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: -4.01 (0.20), residues: 1132 helix: -4.36 (0.12), residues: 390 sheet: -0.81 (0.28), residues: 295 loop : -2.09 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP R 276 HIS 0.008 0.002 HIS R 258 PHE 0.024 0.003 PHE B 234 TYR 0.048 0.003 TYR B 105 ARG 0.014 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.995 Fit side-chains REVERT: A 35 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8227 (mtpt) REVERT: A 209 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7636 (tpp80) REVERT: A 252 ASP cc_start: 0.7529 (t0) cc_final: 0.7306 (t0) REVERT: A 271 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7507 (mptp) REVERT: A 309 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7213 (mt-10) REVERT: R 65 MET cc_start: 0.6998 (mtp) cc_final: 0.6746 (mtp) REVERT: R 70 ARG cc_start: 0.6766 (ttt180) cc_final: 0.6444 (ttt90) REVERT: R 326 MET cc_start: 0.6695 (mmm) cc_final: 0.6355 (mmt) REVERT: R 328 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7113 (mptp) REVERT: G 21 MET cc_start: 0.6579 (tpt) cc_final: 0.6049 (pp-130) REVERT: G 38 MET cc_start: 0.8176 (ttp) cc_final: 0.7920 (ttp) REVERT: S 3 GLN cc_start: 0.7676 (pt0) cc_final: 0.7438 (pt0) REVERT: S 147 CYS cc_start: 0.7079 (t) cc_final: 0.6755 (t) REVERT: B 254 ASP cc_start: 0.8484 (p0) cc_final: 0.8156 (p0) REVERT: B 258 ASP cc_start: 0.7730 (t0) cc_final: 0.7195 (t70) outliers start: 8 outliers final: 1 residues processed: 141 average time/residue: 1.3464 time to fit residues: 201.5173 Evaluate side-chains 109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 312 ASN A 330 ASN R 79 ASN R 196 ASN R 324 ASN G 11 GLN S 130 GLN B 13 GLN B 32 GLN B 155 ASN B 239 ASN B 340 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132177 restraints weight = 10286.324| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.99 r_work: 0.3377 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9274 Z= 0.185 Angle : 0.580 6.666 12570 Z= 0.309 Chirality : 0.043 0.246 1435 Planarity : 0.006 0.136 1577 Dihedral : 8.307 108.946 1392 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 2.76 % Allowed : 10.71 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.23), residues: 1132 helix: -1.84 (0.22), residues: 386 sheet: -0.19 (0.30), residues: 294 loop : -1.59 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 280 PHE 0.020 0.001 PHE R 119 TYR 0.021 0.001 TYR A 297 ARG 0.007 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.035 Fit side-chains REVERT: A 21 LYS cc_start: 0.8170 (tttt) cc_final: 0.7872 (ttmm) REVERT: A 35 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8048 (mtpt) REVERT: A 209 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.6332 (ttp-110) REVERT: A 295 ASN cc_start: 0.7367 (t0) cc_final: 0.6707 (m110) REVERT: A 309 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7208 (mt-10) REVERT: R 70 ARG cc_start: 0.6891 (ttt180) cc_final: 0.6344 (ttt90) REVERT: R 308 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7324 (m) REVERT: R 326 MET cc_start: 0.7549 (mmm) cc_final: 0.7130 (mmt) REVERT: R 328 LYS cc_start: 0.7373 (mmtt) cc_final: 0.6903 (mptp) REVERT: S 83 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8034 (mtp) REVERT: B 219 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7103 (mmt90) REVERT: B 258 ASP cc_start: 0.7952 (t0) cc_final: 0.7213 (t70) REVERT: B 260 GLU cc_start: 0.7927 (pt0) cc_final: 0.7625 (tt0) outliers start: 27 outliers final: 9 residues processed: 139 average time/residue: 1.2566 time to fit residues: 186.6626 Evaluate side-chains 111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** G 11 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 = 0.3870 r_free = 0.3870 target = 0.164573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128441 restraints weight = 9951.193| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.04 r_work: 0.3264 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9274 Z= 0.201 Angle : 0.560 6.601 12570 Z= 0.295 Chirality : 0.043 0.222 1435 Planarity : 0.005 0.131 1577 Dihedral : 7.451 84.491 1390 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 3.06 % Allowed : 13.67 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.11 (0.24), residues: 1132 helix: -0.51 (0.25), residues: 388 sheet: 0.01 (0.30), residues: 294 loop : -1.32 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 109 HIS 0.004 0.001 HIS S 35 PHE 0.023 0.001 PHE R 119 TYR 0.018 0.001 TYR R 313 ARG 0.005 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.002 Fit side-chains REVERT: A 5 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7739 (mm) REVERT: A 21 LYS cc_start: 0.8159 (tttt) cc_final: 0.7883 (ttmm) REVERT: A 35 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8125 (mtpt) REVERT: A 55 ILE cc_start: 0.7400 (mp) cc_final: 0.7173 (mp) REVERT: A 188 THR cc_start: 0.8462 (m) cc_final: 0.8181 (p) REVERT: A 209 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.6412 (ttp-110) REVERT: A 309 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7269 (mt-10) REVERT: R 70 ARG cc_start: 0.6927 (ttt180) cc_final: 0.6411 (ttt90) REVERT: R 264 MET cc_start: 0.6506 (mmm) cc_final: 0.6225 (mmm) REVERT: R 308 SER cc_start: 0.7683 (OUTLIER) cc_final: 0.7286 (m) REVERT: R 326 MET cc_start: 0.7537 (mmm) cc_final: 0.7131 (mmt) REVERT: R 328 LYS cc_start: 0.7445 (mmtt) cc_final: 0.7117 (mptp) REVERT: G 42 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: S 83 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.7797 (mtp) REVERT: B 219 ARG cc_start: 0.7677 (mtm180) cc_final: 0.7158 (mmt90) REVERT: B 258 ASP cc_start: 0.7891 (t0) cc_final: 0.7330 (t70) REVERT: B 260 GLU cc_start: 0.8016 (pt0) cc_final: 0.7689 (tt0) outliers start: 30 outliers final: 10 residues processed: 134 average time/residue: 1.2031 time to fit residues: 172.5023 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 173 CYS Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN R 257 ASN R 302 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131776 restraints weight = 10373.041| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.05 r_work: 0.3356 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9274 Z= 0.206 Angle : 0.556 7.562 12570 Z= 0.292 Chirality : 0.043 0.206 1435 Planarity : 0.005 0.125 1577 Dihedral : 6.954 68.350 1390 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 3.88 % Allowed : 13.57 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.62 (0.24), residues: 1132 helix: 0.16 (0.27), residues: 388 sheet: 0.10 (0.30), residues: 292 loop : -1.16 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.023 0.001 PHE R 119 TYR 0.016 0.001 TYR R 313 ARG 0.004 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.942 Fit side-chains REVERT: A 5 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7692 (mm) REVERT: A 21 LYS cc_start: 0.8092 (tttt) cc_final: 0.7793 (ttmm) REVERT: A 35 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8059 (mtpt) REVERT: A 209 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.6222 (ttp-110) REVERT: A 248 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7236 (mt) REVERT: A 309 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7268 (mt-10) REVERT: R 70 ARG cc_start: 0.6791 (ttt180) cc_final: 0.6312 (ttt90) REVERT: R 264 MET cc_start: 0.6519 (mmm) cc_final: 0.6222 (mmm) REVERT: R 308 SER cc_start: 0.7543 (OUTLIER) cc_final: 0.7075 (m) REVERT: R 326 MET cc_start: 0.7500 (mmm) cc_final: 0.7086 (mmt) REVERT: R 328 LYS cc_start: 0.7330 (mmtt) cc_final: 0.6989 (mptp) REVERT: G 42 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: S 83 MET cc_start: 0.8592 (mtp) cc_final: 0.7785 (mtp) REVERT: B 219 ARG cc_start: 0.7577 (mtm180) cc_final: 0.7066 (mmt90) REVERT: B 258 ASP cc_start: 0.7917 (t0) cc_final: 0.7189 (t70) REVERT: B 260 GLU cc_start: 0.8116 (pt0) cc_final: 0.7764 (tt0) outliers start: 38 outliers final: 18 residues processed: 131 average time/residue: 1.1756 time to fit residues: 165.2441 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 173 CYS Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 55.0886 > 50: distance: 39 - 58: 16.282 distance: 44 - 66: 17.253 distance: 48 - 74: 22.744 distance: 54 - 58: 19.080 distance: 58 - 59: 8.042 distance: 59 - 60: 6.680 distance: 59 - 62: 12.622 distance: 60 - 61: 27.631 distance: 60 - 66: 20.608 distance: 61 - 89: 16.155 distance: 62 - 63: 18.846 distance: 63 - 64: 8.116 distance: 63 - 65: 16.569 distance: 66 - 67: 17.595 distance: 67 - 68: 33.927 distance: 67 - 70: 11.293 distance: 68 - 69: 15.985 distance: 68 - 74: 39.436 distance: 69 - 98: 21.036 distance: 70 - 71: 20.321 distance: 70 - 72: 16.534 distance: 71 - 73: 14.306 distance: 74 - 75: 19.514 distance: 75 - 76: 31.086 distance: 76 - 77: 37.311 distance: 76 - 78: 24.114 distance: 77 - 106: 20.803 distance: 78 - 79: 5.571 distance: 79 - 80: 15.683 distance: 79 - 82: 9.959 distance: 80 - 81: 15.948 distance: 80 - 89: 10.667 distance: 82 - 83: 10.602 distance: 83 - 84: 5.925 distance: 84 - 85: 4.077 distance: 85 - 86: 3.956 distance: 86 - 88: 4.535 distance: 89 - 90: 5.264 distance: 90 - 91: 13.677 distance: 90 - 93: 17.538 distance: 91 - 92: 13.347 distance: 91 - 98: 11.719 distance: 93 - 94: 8.289 distance: 94 - 95: 7.674 distance: 95 - 96: 3.272 distance: 98 - 99: 14.010 distance: 99 - 100: 17.791 distance: 99 - 102: 13.013 distance: 100 - 101: 27.548 distance: 100 - 106: 18.843 distance: 102 - 103: 12.200 distance: 103 - 104: 8.318 distance: 103 - 105: 10.378 distance: 106 - 107: 15.887 distance: 107 - 108: 6.725 distance: 107 - 110: 16.600 distance: 108 - 109: 8.944 distance: 108 - 120: 21.709 distance: 110 - 111: 6.793 distance: 111 - 112: 3.049 distance: 111 - 113: 4.130 distance: 112 - 114: 6.195 distance: 113 - 115: 4.505 distance: 113 - 116: 3.665 distance: 115 - 117: 3.717 distance: 116 - 118: 3.566 distance: 118 - 119: 3.634 distance: 120 - 121: 19.185 distance: 121 - 122: 34.707 distance: 121 - 124: 34.303 distance: 122 - 123: 32.739 distance: 122 - 131: 38.115 distance: 124 - 125: 34.508 distance: 125 - 126: 24.182 distance: 126 - 127: 9.475 distance: 127 - 128: 5.489 distance: 128 - 130: 3.035 distance: 131 - 132: 15.180 distance: 132 - 133: 6.462 distance: 132 - 135: 39.786 distance: 133 - 134: 20.498 distance: 133 - 142: 22.065 distance: 135 - 136: 19.204 distance: 136 - 137: 12.913 distance: 142 - 143: 8.327 distance: 143 - 146: 6.484 distance: 144 - 145: 8.194 distance: 144 - 153: 5.321 distance: 146 - 147: 5.057 distance: 147 - 148: 3.456