Starting phenix.real_space_refine on Sun Aug 24 14:24:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2i_18848/08_2025/8r2i_18848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2i_18848/08_2025/8r2i_18848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r2i_18848/08_2025/8r2i_18848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2i_18848/08_2025/8r2i_18848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r2i_18848/08_2025/8r2i_18848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2i_18848/08_2025/8r2i_18848.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 1 5.49 5 Mg 35 5.21 5 S 61 5.16 5 C 12425 2.51 5 N 2636 2.21 5 O 2894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18054 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2390 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "B" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3811 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 25, 'TRANS': 461} Chain: "C" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3292 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 23, 'TRANS': 399} Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2674 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Chain: "E" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "F" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 269 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 2, 'TRANS': 30} Chain: "H" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 497 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "I" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "2" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "1" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 224 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "A" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 294 Unusual residues: {'BCR': 1, 'BOG': 1, 'CLA': 3, 'FE2': 1, 'PHO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1195 Unusual residues: {'BCR': 2, 'CLA': 16, 'LHG': 1, 'LMG': 1, 'LMT': 2} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 977 Unusual residues: {'BCR': 3, 'BOG': 1, 'CLA': 13, 'DGD': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 359 Unusual residues: {'BCR': 1, 'BCT': 1, 'BOG': 1, 'CLA': 3, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.23 Number of scatterers: 18054 At special positions: 0 Unit cell: (134.4, 107.52, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 61 16.00 P 1 15.00 Mg 35 11.99 O 2894 8.00 N 2636 7.00 C 12425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=34, symmetry=0 Number of additional bonds: simple=34, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 730.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3462 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 66.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 30 through 54 removed outlier: 3.699A pdb=" N ILE A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.840A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 4.217A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 175 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 267 through 295 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 316 through 333 Processing helix chain 'B' and resid 7 through 13 removed outlier: 3.901A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 219 removed outlier: 4.009A pdb=" N ILE B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 233 through 259 removed outlier: 3.882A pdb=" N VAL B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.788A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.520A pdb=" N GLU B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.599A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.567A pdb=" N ILE C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 62 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.634A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 122 removed outlier: 3.561A pdb=" N PHE C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 169 Processing helix chain 'C' and resid 178 through 182 removed outlier: 3.588A pdb=" N GLY C 181 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY C 182 " --> pdb=" O PRO C 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 182' Processing helix chain 'C' and resid 193 through 203 removed outlier: 4.120A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.819A pdb=" N SER C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 removed outlier: 3.540A pdb=" N ILE C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 313 removed outlier: 3.909A pdb=" N SER C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 347 removed outlier: 3.731A pdb=" N THR C 343 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP C 347 " --> pdb=" O MET C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.706A pdb=" N LYS C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 33 through 54 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.106A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.561A pdb=" N ILE D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.526A pdb=" N PHE D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 194 through 218 Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 298 through 308 removed outlier: 3.662A pdb=" N GLU D 302 " --> pdb=" O PHE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 334 removed outlier: 4.449A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'E' and resid 9 through 15 removed outlier: 4.071A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 9 through 15' Processing helix chain 'E' and resid 18 through 40 removed outlier: 3.952A pdb=" N SER E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 48 Processing helix chain 'E' and resid 71 through 80 removed outlier: 3.803A pdb=" N GLN E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 41 Proline residue: F 28 - end of helix removed outlier: 3.985A pdb=" N PHE F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 35 Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 46 through 69 Processing helix chain 'I' and resid 2 through 24 Processing helix chain 'K' and resid 12 through 17 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 18 through 25 Processing helix chain 'K' and resid 27 through 44 Processing helix chain '2' and resid 32 through 50 removed outlier: 3.732A pdb=" N GLU 2 36 " --> pdb=" O THR 2 32 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU 2 50 " --> pdb=" O VAL 2 46 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 76 removed outlier: 3.845A pdb=" N GLU 2 58 " --> pdb=" O ASP 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 78 through 83 Processing helix chain '2' and resid 84 through 103 removed outlier: 3.546A pdb=" N SER 2 103 " --> pdb=" O GLY 2 99 " (cutoff:3.500A) Processing helix chain '2' and resid 111 through 130 removed outlier: 3.892A pdb=" N THR 2 130 " --> pdb=" O THR 2 126 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 15 removed outlier: 3.539A pdb=" N ALA 1 6 " --> pdb=" O ASN 1 2 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL 1 15 " --> pdb=" O SER 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 24 removed outlier: 3.710A pdb=" N VAL 1 22 " --> pdb=" O ALA 1 18 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AA2, first strand: chain 'B' and resid 322 through 323 removed outlier: 7.509A pdb=" N GLY B 322 " --> pdb=" O ARG D 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 336 through 340 removed outlier: 5.725A pdb=" N ALA B 337 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP B 433 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 339 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.703A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'C' and resid 330 through 331 Processing sheet with id=AA7, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.799A pdb=" N GLY C 362 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 77 through 78 897 hydrogen bonds defined for protein. 2577 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: 3.01 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 7863 1.41 - 1.61: 10694 1.61 - 1.81: 137 1.81 - 2.01: 35 2.01 - 2.21: 109 Bond restraints: 18838 Sorted by residual: bond pdb=" C25 BCR B 517 " pdb=" C26 BCR B 517 " ideal model delta sigma weight residual 1.347 1.611 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C25 BCR H 101 " pdb=" C26 BCR H 101 " ideal model delta sigma weight residual 1.347 1.608 -0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C25 BCR C 515 " pdb=" C26 BCR C 515 " ideal model delta sigma weight residual 1.347 1.607 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C25 BCR C 516 " pdb=" C26 BCR C 516 " ideal model delta sigma weight residual 1.347 1.606 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C25 BCR A 406 " pdb=" C26 BCR A 406 " ideal model delta sigma weight residual 1.347 1.606 -0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 18833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.48: 26049 9.48 - 18.96: 93 18.96 - 28.44: 0 28.44 - 37.92: 0 37.92 - 47.40: 6 Bond angle restraints: 26148 Sorted by residual: angle pdb=" CBD CLA C 513 " pdb=" CGD CLA C 513 " pdb=" O1D CLA C 513 " ideal model delta sigma weight residual 127.77 80.37 47.40 3.00e+00 1.11e-01 2.50e+02 angle pdb=" CBD CLA C 513 " pdb=" CGD CLA C 513 " pdb=" O2D CLA C 513 " ideal model delta sigma weight residual 113.93 159.37 -45.44 3.00e+00 1.11e-01 2.29e+02 angle pdb=" C2 CLA B 502 " pdb=" C3 CLA B 502 " pdb=" C4 CLA B 502 " ideal model delta sigma weight residual 122.00 81.82 40.18 3.00e+00 1.11e-01 1.79e+02 angle pdb=" C4 CLA B 502 " pdb=" C3 CLA B 502 " pdb=" C5 CLA B 502 " ideal model delta sigma weight residual 117.04 77.09 39.95 3.00e+00 1.11e-01 1.77e+02 angle pdb=" O1D CLA C 513 " pdb=" CGD CLA C 513 " pdb=" O2D CLA C 513 " ideal model delta sigma weight residual 118.28 79.12 39.16 3.00e+00 1.11e-01 1.70e+02 ... (remaining 26143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.55: 9341 32.55 - 65.11: 445 65.11 - 97.66: 49 97.66 - 130.22: 78 130.22 - 162.77: 1 Dihedral angle restraints: 9914 sinusoidal: 4482 harmonic: 5432 Sorted by residual: dihedral pdb=" C3A DGD C 517 " pdb=" C1A DGD C 517 " pdb=" C2A DGD C 517 " pdb=" O1A DGD C 517 " ideal model delta sinusoidal sigma weight residual 335.78 173.01 162.77 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4D PHO D 402 " pdb=" CBD PHO D 402 " pdb=" CHA PHO D 402 " pdb=" CGD PHO D 402 " ideal model delta sinusoidal sigma weight residual 243.52 115.98 127.54 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CA THR D 217 " pdb=" C THR D 217 " pdb=" N VAL D 218 " pdb=" CA VAL D 218 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 9911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 2475 0.154 - 0.308: 7 0.308 - 0.461: 0 0.461 - 0.615: 11 0.615 - 0.769: 24 Chirality restraints: 2517 Sorted by residual: chirality pdb=" C3A CLA B 504 " pdb=" C2A CLA B 504 " pdb=" C4A CLA B 504 " pdb=" CMA CLA B 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.00 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C3A CLA C 504 " pdb=" C2A CLA C 504 " pdb=" C4A CLA C 504 " pdb=" CMA CLA C 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.02 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C3A CLA C 511 " pdb=" C2A CLA C 511 " pdb=" C4A CLA C 511 " pdb=" CMA CLA C 511 " both_signs ideal model delta sigma weight residual False -2.76 -2.04 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 2514 not shown) Planarity restraints: 3296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO A 404 " -0.094 2.00e-02 2.50e+03 1.12e-01 1.01e+03 pdb=" ND PHO A 404 " -0.055 2.00e-02 2.50e+03 pdb=" C1A PHO A 404 " -0.014 2.00e-02 2.50e+03 pdb=" C1B PHO A 404 " -0.044 2.00e-02 2.50e+03 pdb=" C1C PHO A 404 " -0.020 2.00e-02 2.50e+03 pdb=" C1D PHO A 404 " 0.009 2.00e-02 2.50e+03 pdb=" C2A PHO A 404 " 0.097 2.00e-02 2.50e+03 pdb=" C2B PHO A 404 " 0.113 2.00e-02 2.50e+03 pdb=" C2C PHO A 404 " -0.063 2.00e-02 2.50e+03 pdb=" C2D PHO A 404 " 0.053 2.00e-02 2.50e+03 pdb=" C3A PHO A 404 " -0.288 2.00e-02 2.50e+03 pdb=" C3B PHO A 404 " 0.142 2.00e-02 2.50e+03 pdb=" C3C PHO A 404 " -0.060 2.00e-02 2.50e+03 pdb=" C3D PHO A 404 " 0.056 2.00e-02 2.50e+03 pdb=" C4A PHO A 404 " -0.193 2.00e-02 2.50e+03 pdb=" C4B PHO A 404 " 0.006 2.00e-02 2.50e+03 pdb=" C4C PHO A 404 " -0.007 2.00e-02 2.50e+03 pdb=" C4D PHO A 404 " 0.005 2.00e-02 2.50e+03 pdb=" CAB PHO A 404 " 0.263 2.00e-02 2.50e+03 pdb=" CAC PHO A 404 " -0.096 2.00e-02 2.50e+03 pdb=" CAD PHO A 404 " 0.081 2.00e-02 2.50e+03 pdb=" CBD PHO A 404 " 0.104 2.00e-02 2.50e+03 pdb=" CHA PHO A 404 " 0.028 2.00e-02 2.50e+03 pdb=" CHB PHO A 404 " -0.125 2.00e-02 2.50e+03 pdb=" CHC PHO A 404 " -0.022 2.00e-02 2.50e+03 pdb=" CHD PHO A 404 " 0.028 2.00e-02 2.50e+03 pdb=" CMB PHO A 404 " 0.192 2.00e-02 2.50e+03 pdb=" CMC PHO A 404 " -0.110 2.00e-02 2.50e+03 pdb=" CMD PHO A 404 " 0.095 2.00e-02 2.50e+03 pdb=" NA PHO A 404 " -0.183 2.00e-02 2.50e+03 pdb=" NC PHO A 404 " 0.017 2.00e-02 2.50e+03 pdb=" OBD PHO A 404 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 402 " 0.037 2.00e-02 2.50e+03 5.50e-02 2.42e+02 pdb=" ND PHO D 402 " 0.126 2.00e-02 2.50e+03 pdb=" C1A PHO D 402 " 0.012 2.00e-02 2.50e+03 pdb=" C1B PHO D 402 " 0.007 2.00e-02 2.50e+03 pdb=" C1C PHO D 402 " 0.018 2.00e-02 2.50e+03 pdb=" C1D PHO D 402 " 0.020 2.00e-02 2.50e+03 pdb=" C2A PHO D 402 " 0.147 2.00e-02 2.50e+03 pdb=" C2B PHO D 402 " 0.007 2.00e-02 2.50e+03 pdb=" C2C PHO D 402 " 0.004 2.00e-02 2.50e+03 pdb=" C2D PHO D 402 " -0.004 2.00e-02 2.50e+03 pdb=" C3A PHO D 402 " -0.106 2.00e-02 2.50e+03 pdb=" C3B PHO D 402 " 0.024 2.00e-02 2.50e+03 pdb=" C3C PHO D 402 " -0.029 2.00e-02 2.50e+03 pdb=" C3D PHO D 402 " 0.015 2.00e-02 2.50e+03 pdb=" C4A PHO D 402 " -0.076 2.00e-02 2.50e+03 pdb=" C4B PHO D 402 " 0.038 2.00e-02 2.50e+03 pdb=" C4C PHO D 402 " -0.029 2.00e-02 2.50e+03 pdb=" C4D PHO D 402 " 0.050 2.00e-02 2.50e+03 pdb=" CAB PHO D 402 " 0.014 2.00e-02 2.50e+03 pdb=" CAC PHO D 402 " -0.058 2.00e-02 2.50e+03 pdb=" CAD PHO D 402 " 0.010 2.00e-02 2.50e+03 pdb=" CBD PHO D 402 " -0.079 2.00e-02 2.50e+03 pdb=" CHA PHO D 402 " -0.004 2.00e-02 2.50e+03 pdb=" CHB PHO D 402 " -0.020 2.00e-02 2.50e+03 pdb=" CHC PHO D 402 " 0.040 2.00e-02 2.50e+03 pdb=" CHD PHO D 402 " -0.052 2.00e-02 2.50e+03 pdb=" CMB PHO D 402 " -0.028 2.00e-02 2.50e+03 pdb=" CMC PHO D 402 " 0.014 2.00e-02 2.50e+03 pdb=" CMD PHO D 402 " -0.043 2.00e-02 2.50e+03 pdb=" NA PHO D 402 " -0.113 2.00e-02 2.50e+03 pdb=" NC PHO D 402 " 0.001 2.00e-02 2.50e+03 pdb=" OBD PHO D 402 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3D CLA A 402 " -0.044 2.00e-02 2.50e+03 8.52e-02 7.26e+01 pdb=" CAD CLA A 402 " 0.147 2.00e-02 2.50e+03 pdb=" CBD CLA A 402 " -0.042 2.00e-02 2.50e+03 pdb=" OBD CLA A 402 " -0.061 2.00e-02 2.50e+03 ... (remaining 3293 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1924 2.75 - 3.29: 17605 3.29 - 3.82: 32570 3.82 - 4.36: 38321 4.36 - 4.90: 65677 Nonbonded interactions: 156097 Sorted by model distance: nonbonded pdb=" O THR 2 47 " pdb=" NZ LYS 2 57 " model vdw 2.210 3.120 nonbonded pdb=" O TYR A 29 " pdb=" NH1 ARG A 129 " model vdw 2.251 3.120 nonbonded pdb=" OH TYR E 19 " pdb=" O SER 1 17 " model vdw 2.255 3.040 nonbonded pdb=" O TRP C 238 " pdb=" OG1 THR C 242 " model vdw 2.267 3.040 nonbonded pdb=" NH1 ARG B 124 " pdb=" O GLU H 19 " model vdw 2.270 3.120 ... (remaining 156092 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.090 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.026 0.686 18872 Z= 1.876 Angle : 1.619 47.403 26148 Z= 0.573 Chirality : 0.088 0.769 2517 Planarity : 0.008 0.112 3296 Dihedral : 21.202 162.774 6452 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.20), residues: 1897 helix: 1.83 (0.15), residues: 1142 sheet: 0.33 (0.96), residues: 32 loop : -0.12 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 8 TYR 0.016 0.001 TYR H 68 PHE 0.039 0.001 PHE D 185 TRP 0.015 0.001 TRP A 131 HIS 0.007 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.02117 (18838) covalent geometry : angle 1.61908 (26148) hydrogen bonds : bond 0.11816 ( 897) hydrogen bonds : angle 5.69481 ( 2577) Misc. bond : bond 0.37142 ( 34) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.487 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.6572 time to fit residues: 122.2508 Evaluate side-chains 114 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 0.0050 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059985 restraints weight = 45107.249| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.28 r_work: 0.2817 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 18872 Z= 0.118 Angle : 0.919 44.200 26148 Z= 0.356 Chirality : 0.042 0.377 2517 Planarity : 0.004 0.056 3296 Dihedral : 20.721 165.410 3212 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.32 % Allowed : 7.72 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.20), residues: 1897 helix: 1.99 (0.15), residues: 1139 sheet: -0.85 (0.81), residues: 42 loop : -0.01 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.012 0.001 TYR H 68 PHE 0.025 0.001 PHE B 246 TRP 0.013 0.001 TRP C 51 HIS 0.004 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00242 (18838) covalent geometry : angle 0.91900 (26148) hydrogen bonds : bond 0.04269 ( 897) hydrogen bonds : angle 4.63141 ( 2577) Misc. bond : bond 0.01640 ( 34) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.488 Fit side-chains REVERT: A 59 ASP cc_start: 0.8783 (p0) cc_final: 0.8264 (p0) REVERT: A 104 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8690 (tm-30) REVERT: B 60 MET cc_start: 0.9420 (mmp) cc_final: 0.8997 (mmp) REVERT: D 225 ASP cc_start: 0.6741 (t70) cc_final: 0.6172 (p0) REVERT: E 17 ILE cc_start: 0.7771 (mm) cc_final: 0.7398 (tp) REVERT: E 24 SER cc_start: 0.8739 (m) cc_final: 0.8329 (p) REVERT: E 77 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8183 (tmtt) REVERT: H 36 GLU cc_start: 0.7370 (tt0) cc_final: 0.6897 (tp30) REVERT: K 24 VAL cc_start: 0.9202 (t) cc_final: 0.8956 (p) REVERT: 2 45 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8197 (mttp) outliers start: 5 outliers final: 3 residues processed: 140 average time/residue: 0.4861 time to fit residues: 77.7652 Evaluate side-chains 124 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 14 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 84 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 HIS D 189 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.054935 restraints weight = 46495.495| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.30 r_work: 0.2682 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 18872 Z= 0.240 Angle : 0.952 44.527 26148 Z= 0.380 Chirality : 0.045 0.285 2517 Planarity : 0.005 0.058 3296 Dihedral : 17.729 167.324 3212 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.22 % Allowed : 9.01 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.19), residues: 1897 helix: 1.88 (0.15), residues: 1122 sheet: -0.38 (0.95), residues: 35 loop : -0.06 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 472 TYR 0.024 0.002 TYR H 68 PHE 0.027 0.002 PHE B 246 TRP 0.014 0.001 TRP A 131 HIS 0.005 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00559 (18838) covalent geometry : angle 0.95235 (26148) hydrogen bonds : bond 0.05073 ( 897) hydrogen bonds : angle 4.69385 ( 2577) Misc. bond : bond 0.02986 ( 34) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.648 Fit side-chains REVERT: A 104 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8772 (tm-30) REVERT: D 225 ASP cc_start: 0.6787 (t70) cc_final: 0.6177 (p0) REVERT: E 17 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7558 (tp) REVERT: E 62 GLU cc_start: 0.8599 (mp0) cc_final: 0.8213 (pm20) REVERT: E 77 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8192 (tmtt) REVERT: H 36 GLU cc_start: 0.7896 (tt0) cc_final: 0.7198 (tp30) REVERT: K 24 VAL cc_start: 0.9229 (t) cc_final: 0.9005 (p) outliers start: 19 outliers final: 5 residues processed: 126 average time/residue: 0.5896 time to fit residues: 84.1441 Evaluate side-chains 111 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 142 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.077116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.057226 restraints weight = 45880.230| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.27 r_work: 0.2732 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 18872 Z= 0.134 Angle : 0.884 44.312 26148 Z= 0.345 Chirality : 0.041 0.254 2517 Planarity : 0.004 0.057 3296 Dihedral : 16.274 170.549 3212 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.84 % Allowed : 10.62 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.19), residues: 1897 helix: 1.94 (0.15), residues: 1144 sheet: -0.56 (0.91), residues: 37 loop : -0.06 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 345 TYR 0.018 0.001 TYR H 68 PHE 0.022 0.001 PHE B 246 TRP 0.013 0.001 TRP A 131 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00299 (18838) covalent geometry : angle 0.88381 (26148) hydrogen bonds : bond 0.04291 ( 897) hydrogen bonds : angle 4.47750 ( 2577) Misc. bond : bond 0.01846 ( 34) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.470 Fit side-chains REVERT: A 59 ASP cc_start: 0.8761 (p0) cc_final: 0.8526 (p0) REVERT: A 104 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8773 (tm-30) REVERT: D 225 ASP cc_start: 0.6789 (t70) cc_final: 0.6183 (p0) REVERT: E 8 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.7729 (ttt180) REVERT: E 17 ILE cc_start: 0.7894 (mm) cc_final: 0.7639 (tp) REVERT: E 24 SER cc_start: 0.8641 (m) cc_final: 0.8170 (p) REVERT: E 62 GLU cc_start: 0.8604 (mp0) cc_final: 0.8133 (pm20) REVERT: E 77 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8151 (tmtt) REVERT: H 36 GLU cc_start: 0.7759 (tt0) cc_final: 0.7168 (tp30) REVERT: H 76 ASP cc_start: 0.7627 (t70) cc_final: 0.7397 (t0) REVERT: K 24 VAL cc_start: 0.9232 (t) cc_final: 0.9008 (p) outliers start: 13 outliers final: 7 residues processed: 124 average time/residue: 0.5204 time to fit residues: 73.4906 Evaluate side-chains 119 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 101 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 220 ASN ** 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 = 0.3313 r_free = 0.3313 target = 0.076845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056456 restraints weight = 45966.307| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.28 r_work: 0.2722 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 18872 Z= 0.144 Angle : 0.875 44.378 26148 Z= 0.342 Chirality : 0.041 0.251 2517 Planarity : 0.004 0.057 3296 Dihedral : 15.618 172.193 3212 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.42 % Allowed : 11.00 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.19), residues: 1897 helix: 1.97 (0.15), residues: 1144 sheet: -0.57 (0.89), residues: 37 loop : -0.03 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 177 TYR 0.015 0.001 TYR H 68 PHE 0.022 0.001 PHE B 246 TRP 0.014 0.001 TRP A 131 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00326 (18838) covalent geometry : angle 0.87501 (26148) hydrogen bonds : bond 0.04307 ( 897) hydrogen bonds : angle 4.40867 ( 2577) Misc. bond : bond 0.02069 ( 34) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8743 (p0) cc_final: 0.8509 (p0) REVERT: A 104 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8755 (tm-30) REVERT: B 60 MET cc_start: 0.9525 (mmp) cc_final: 0.8994 (mmp) REVERT: C 402 ILE cc_start: 0.2356 (OUTLIER) cc_final: 0.2093 (pp) REVERT: D 225 ASP cc_start: 0.6847 (t70) cc_final: 0.6279 (p0) REVERT: E 8 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.7771 (ttt180) REVERT: E 17 ILE cc_start: 0.7977 (mm) cc_final: 0.7715 (tp) REVERT: E 24 SER cc_start: 0.8721 (m) cc_final: 0.8291 (p) REVERT: E 77 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8168 (tmtt) REVERT: H 36 GLU cc_start: 0.7838 (tt0) cc_final: 0.7270 (tp30) REVERT: H 76 ASP cc_start: 0.7650 (t70) cc_final: 0.7433 (t0) REVERT: K 24 VAL cc_start: 0.9218 (t) cc_final: 0.9009 (p) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.5240 time to fit residues: 78.6577 Evaluate side-chains 124 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain 2 residue 50 LEU Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 16 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 91 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 220 ASN ** 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 = 0.3315 r_free = 0.3315 target = 0.076783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056980 restraints weight = 45593.812| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.25 r_work: 0.2725 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 18872 Z= 0.144 Angle : 0.868 44.387 26148 Z= 0.340 Chirality : 0.041 0.255 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.350 172.139 3212 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.22 % Allowed : 12.23 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.19), residues: 1897 helix: 2.01 (0.15), residues: 1138 sheet: -0.40 (0.93), residues: 35 loop : -0.04 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.014 0.001 TYR H 68 PHE 0.023 0.001 PHE B 246 TRP 0.013 0.001 TRP A 131 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00327 (18838) covalent geometry : angle 0.86810 (26148) hydrogen bonds : bond 0.04239 ( 897) hydrogen bonds : angle 4.37955 ( 2577) Misc. bond : bond 0.02064 ( 34) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8734 (p0) cc_final: 0.8504 (p0) REVERT: A 98 GLU cc_start: 0.8729 (tt0) cc_final: 0.8526 (mm-30) REVERT: A 104 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8773 (tm-30) REVERT: B 60 MET cc_start: 0.9538 (mmp) cc_final: 0.8916 (mmp) REVERT: C 402 ILE cc_start: 0.2422 (OUTLIER) cc_final: 0.2163 (pp) REVERT: D 225 ASP cc_start: 0.6874 (t70) cc_final: 0.6315 (p0) REVERT: E 8 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7809 (ttt180) REVERT: E 17 ILE cc_start: 0.7981 (mm) cc_final: 0.7730 (tp) REVERT: E 24 SER cc_start: 0.8740 (m) cc_final: 0.8324 (p) REVERT: E 62 GLU cc_start: 0.8614 (mp0) cc_final: 0.8215 (pm20) REVERT: E 77 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8162 (tmtt) REVERT: H 36 GLU cc_start: 0.7916 (tt0) cc_final: 0.7632 (tt0) REVERT: H 76 ASP cc_start: 0.7729 (t70) cc_final: 0.7472 (t0) REVERT: K 24 VAL cc_start: 0.9225 (t) cc_final: 0.9018 (p) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 0.5080 time to fit residues: 74.2569 Evaluate side-chains 125 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 42 optimal weight: 0.0770 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 0.0670 chunk 101 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 10 optimal weight: 0.0060 overall best weight: 1.0296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 220 ASN ** 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 = 0.3328 r_free = 0.3328 target = 0.077588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.057432 restraints weight = 45784.355| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.28 r_work: 0.2742 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 18872 Z= 0.121 Angle : 0.856 44.308 26148 Z= 0.335 Chirality : 0.040 0.244 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.130 173.852 3212 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.22 % Allowed : 13.06 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.20), residues: 1897 helix: 2.05 (0.15), residues: 1139 sheet: -0.55 (0.89), residues: 37 loop : -0.05 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.011 0.001 TYR H 68 PHE 0.021 0.001 PHE B 246 TRP 0.013 0.001 TRP A 131 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00268 (18838) covalent geometry : angle 0.85562 (26148) hydrogen bonds : bond 0.04037 ( 897) hydrogen bonds : angle 4.29413 ( 2577) Misc. bond : bond 0.01805 ( 34) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8661 (p0) cc_final: 0.8453 (p0) REVERT: A 104 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8809 (tm-30) REVERT: C 402 ILE cc_start: 0.2638 (OUTLIER) cc_final: 0.2373 (pp) REVERT: D 225 ASP cc_start: 0.6895 (t70) cc_final: 0.6336 (p0) REVERT: E 8 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7679 (ttt180) REVERT: E 17 ILE cc_start: 0.7963 (mm) cc_final: 0.7734 (tp) REVERT: E 18 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7174 (ppt170) REVERT: E 24 SER cc_start: 0.8760 (m) cc_final: 0.8344 (p) REVERT: E 62 GLU cc_start: 0.8665 (mp0) cc_final: 0.8233 (pm20) REVERT: E 77 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8170 (tmtt) REVERT: H 36 GLU cc_start: 0.7897 (tt0) cc_final: 0.7604 (tt0) REVERT: H 76 ASP cc_start: 0.7681 (t70) cc_final: 0.7406 (t0) REVERT: K 24 VAL cc_start: 0.9219 (t) cc_final: 0.9017 (p) REVERT: 2 45 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8332 (mttp) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.5297 time to fit residues: 78.7977 Evaluate side-chains 129 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 181 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 42 optimal weight: 0.0040 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 220 ASN ** 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 = 0.3329 r_free = 0.3329 target = 0.077465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.057704 restraints weight = 45433.678| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.28 r_work: 0.2745 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 18872 Z= 0.126 Angle : 0.858 44.355 26148 Z= 0.337 Chirality : 0.040 0.249 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.038 174.754 3212 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.48 % Allowed : 13.13 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.20), residues: 1897 helix: 2.08 (0.15), residues: 1138 sheet: -0.34 (0.93), residues: 35 loop : -0.04 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.011 0.001 TYR H 68 PHE 0.021 0.001 PHE B 246 TRP 0.013 0.001 TRP A 131 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00283 (18838) covalent geometry : angle 0.85794 (26148) hydrogen bonds : bond 0.04035 ( 897) hydrogen bonds : angle 4.27346 ( 2577) Misc. bond : bond 0.01988 ( 34) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8651 (p0) cc_final: 0.8432 (p0) REVERT: A 104 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 329 GLU cc_start: 0.8452 (tp30) cc_final: 0.8246 (tp30) REVERT: C 391 SER cc_start: 0.5240 (OUTLIER) cc_final: 0.5027 (m) REVERT: C 402 ILE cc_start: 0.2650 (OUTLIER) cc_final: 0.2381 (pp) REVERT: D 225 ASP cc_start: 0.7017 (t70) cc_final: 0.6424 (p0) REVERT: E 8 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7660 (ttt180) REVERT: E 17 ILE cc_start: 0.7955 (mm) cc_final: 0.7730 (tp) REVERT: E 18 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7182 (ppt170) REVERT: E 24 SER cc_start: 0.8722 (m) cc_final: 0.8309 (p) REVERT: E 62 GLU cc_start: 0.8658 (mp0) cc_final: 0.8205 (pm20) REVERT: E 77 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8202 (tmtt) REVERT: H 36 GLU cc_start: 0.7864 (tt0) cc_final: 0.7609 (tt0) REVERT: H 76 ASP cc_start: 0.7676 (t70) cc_final: 0.7401 (t0) outliers start: 23 outliers final: 15 residues processed: 134 average time/residue: 0.5495 time to fit residues: 83.7379 Evaluate side-chains 130 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 16 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 103 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** 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 = 0.3344 r_free = 0.3344 target = 0.078319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.058364 restraints weight = 45599.452| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.27 r_work: 0.2765 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 18872 Z= 0.113 Angle : 0.854 44.297 26148 Z= 0.336 Chirality : 0.040 0.242 2517 Planarity : 0.004 0.056 3296 Dihedral : 14.840 176.201 3212 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.35 % Allowed : 13.64 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.20), residues: 1897 helix: 2.12 (0.15), residues: 1138 sheet: -0.49 (0.90), residues: 37 loop : -0.02 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.010 0.001 TYR H 68 PHE 0.020 0.001 PHE B 246 TRP 0.013 0.001 TRP A 131 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00249 (18838) covalent geometry : angle 0.85369 (26148) hydrogen bonds : bond 0.03852 ( 897) hydrogen bonds : angle 4.21567 ( 2577) Misc. bond : bond 0.01820 ( 34) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8723 (tm-30) REVERT: C 402 ILE cc_start: 0.2610 (OUTLIER) cc_final: 0.2352 (pp) REVERT: E 8 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7799 (ttt180) REVERT: E 17 ILE cc_start: 0.7970 (mm) cc_final: 0.7749 (tp) REVERT: E 18 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7223 (ppt170) REVERT: E 24 SER cc_start: 0.8753 (m) cc_final: 0.8336 (p) REVERT: E 62 GLU cc_start: 0.8658 (mp0) cc_final: 0.8196 (pm20) REVERT: E 77 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8170 (tmtt) REVERT: H 36 GLU cc_start: 0.7802 (tt0) cc_final: 0.7557 (tt0) REVERT: H 76 ASP cc_start: 0.7690 (t70) cc_final: 0.7409 (t0) outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 0.5410 time to fit residues: 81.2008 Evaluate side-chains 123 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 129 LEU Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 13 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 141 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.076899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.057151 restraints weight = 45591.818| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.25 r_work: 0.2728 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 18872 Z= 0.149 Angle : 0.872 44.459 26148 Z= 0.345 Chirality : 0.041 0.246 2517 Planarity : 0.004 0.057 3296 Dihedral : 14.912 174.778 3212 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.97 % Allowed : 14.29 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.19), residues: 1897 helix: 2.08 (0.15), residues: 1135 sheet: -0.30 (0.95), residues: 35 loop : -0.03 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.014 0.001 TYR H 68 PHE 0.023 0.001 PHE B 246 TRP 0.013 0.001 TRP A 131 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00343 (18838) covalent geometry : angle 0.87211 (26148) hydrogen bonds : bond 0.04196 ( 897) hydrogen bonds : angle 4.27352 ( 2577) Misc. bond : bond 0.02352 ( 34) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8714 (tm-30) REVERT: C 402 ILE cc_start: 0.2597 (OUTLIER) cc_final: 0.2343 (pp) REVERT: E 8 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7738 (ttt180) REVERT: E 17 ILE cc_start: 0.7978 (mm) cc_final: 0.7768 (tp) REVERT: E 62 GLU cc_start: 0.8624 (mp0) cc_final: 0.8136 (pm20) REVERT: E 77 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8171 (tmtt) REVERT: H 36 GLU cc_start: 0.7902 (tt0) cc_final: 0.7691 (tt0) REVERT: H 76 ASP cc_start: 0.7706 (t70) cc_final: 0.7442 (t0) outliers start: 15 outliers final: 12 residues processed: 123 average time/residue: 0.5460 time to fit residues: 76.1238 Evaluate side-chains 129 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 129 LEU Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 16 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 109 optimal weight: 0.0050 chunk 130 optimal weight: 0.4980 chunk 168 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN D 189 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.058544 restraints weight = 45440.488| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.28 r_work: 0.2775 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 18872 Z= 0.110 Angle : 0.860 44.293 26148 Z= 0.337 Chirality : 0.041 0.487 2517 Planarity : 0.004 0.055 3296 Dihedral : 14.737 177.004 3212 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.97 % Allowed : 13.96 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.20), residues: 1897 helix: 2.16 (0.15), residues: 1138 sheet: -0.68 (0.85), residues: 40 loop : -0.02 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.010 0.001 TYR H 68 PHE 0.021 0.001 PHE B 246 TRP 0.014 0.001 TRP C 51 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00241 (18838) covalent geometry : angle 0.85977 (26148) hydrogen bonds : bond 0.03838 ( 897) hydrogen bonds : angle 4.18030 ( 2577) Misc. bond : bond 0.01776 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4952.78 seconds wall clock time: 85 minutes 22.88 seconds (5122.88 seconds total)