Starting phenix.real_space_refine on Sat Jul 4 11:39:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8r2i_18848/07_2026/8r2i_18848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2i_18848/07_2026/8r2i_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_18848/07_2026/8r2i_18848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2i_18848/07_2026/8r2i_18848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r2i_18848/07_2026/8r2i_18848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2i_18848/07_2026/8r2i_18848.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8r2i_18848/07_2026/8r2i_18848.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8r2i_18848/07_2026/8r2i_18848.cif" } 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-dev-6108/lib/python3.11/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: 3.25, per 1000 atoms: 0.18 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: 1.87 Conformation dependent library (CDL) restraints added in 721.0 milliseconds 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: 0.34 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: 2.80 Time building geometry restraints manager: 2.38 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: 9346 32.55 - 65.11: 448 65.11 - 97.66: 49 97.66 - 130.22: 70 130.22 - 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=" 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 dihedral pdb=" C1 BCR C 515 " pdb=" C2 BCR C 515 " pdb=" C3 BCR C 515 " pdb=" C4 BCR C 515 " ideal model delta sinusoidal sigma weight residual -60.86 62.06 -122.92 1 3.00e+01 1.11e-03 1.65e+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: 3302 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" C1C CLA B 515 " 0.007 2.00e-02 2.50e+03 6.46e-02 6.27e+01 pdb=" C3C CLA B 515 " -0.086 2.00e-02 2.50e+03 pdb=" C4C CLA B 515 " 0.043 2.00e-02 2.50e+03 pdb=" CHD CLA B 515 " 0.004 2.00e-02 2.50e+03 pdb=" NC CLA B 515 " 0.103 2.00e-02 2.50e+03 pdb="MG CLA B 515 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C CLA C 502 " -0.024 2.00e-02 2.50e+03 5.33e-02 4.27e+01 pdb=" C3C CLA C 502 " 0.076 2.00e-02 2.50e+03 pdb=" C4C CLA C 502 " -0.016 2.00e-02 2.50e+03 pdb=" CHD CLA C 502 " -0.021 2.00e-02 2.50e+03 pdb=" NC CLA C 502 " -0.078 2.00e-02 2.50e+03 pdb="MG CLA C 502 " 0.062 2.00e-02 2.50e+03 ... (remaining 3299 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: 3.720 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.340 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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= 1.878 Angle : 1.629 47.403 26148 Z= 0.576 Chirality : 0.088 0.769 2517 Planarity : 0.008 0.085 3302 Dihedral : 20.779 162.774 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 are 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/Z covalent geometry : bond 0.02127 / 1.06 (18838) covalent geometry : angle 1.62945 / 0.58 (26148) hydrogen bonds : bond 0.11816 / 7.74 ( 897) hydrogen bonds : angle 5.69481 / 4.20 ( 2577) Misc. bond : bond 0.37142 / 24.10 ( 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 : 0.579 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.5553 time to fit residues: 103.7541 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 : 0.641 ------------------------------------------------------------------------------- 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... 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 = 0.080217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059961 restraints weight = 45115.139| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.30 r_work: 0.2817 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1033 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= 0.121 Angle : 0.918 44.107 26148 Z= 0.356 Chirality : 0.042 0.428 2517 Planarity : 0.004 0.056 3302 Dihedral : 19.782 165.604 3212 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.39 % Allowed : 7.66 % 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 are not related in a simple way. whole: 1.76 (0.20), residues: 1897 helix: 2.00 (0.15), residues: 1139 sheet: -0.83 (0.81), residues: 42 loop : -0.00 (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 C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (18838) covalent geometry : angle 0.91805 / 0.36 (26148) hydrogen bonds : bond 0.04231 / 2.82 ( 897) hydrogen bonds : angle 4.61941 / 3.41 ( 2577) Misc. bond : bond 0.01568 / 1.33 ( 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 145 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8749 (p0) cc_final: 0.8229 (p0) REVERT: A 104 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8679 (tm-30) REVERT: D 225 ASP cc_start: 0.6810 (t70) cc_final: 0.6221 (p0) REVERT: E 17 ILE cc_start: 0.7738 (mm) cc_final: 0.7374 (tp) REVERT: E 24 SER cc_start: 0.8747 (m) cc_final: 0.8321 (p) REVERT: E 77 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8169 (tmtt) REVERT: H 36 GLU cc_start: 0.7337 (tt0) cc_final: 0.6831 (tp30) REVERT: K 24 VAL cc_start: 0.9198 (t) cc_final: 0.8951 (p) outliers start: 6 outliers final: 4 residues processed: 141 average time/residue: 0.4674 time to fit residues: 75.8155 Evaluate side-chains 123 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain 1 residue 16 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 84 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3307 r_free = 0.3307 target = 0.076678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.056046 restraints weight = 46168.765| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.31 r_work: 0.2710 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 18872 Z= 0.191 Angle : 0.923 44.381 26148 Z= 0.363 Chirality : 0.043 0.251 2517 Planarity : 0.004 0.057 3302 Dihedral : 16.548 167.138 3212 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.09 % Allowed : 9.20 % Favored : 89.70 % 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 are not related in a simple way. whole: 1.68 (0.20), residues: 1897 helix: 1.93 (0.15), residues: 1136 sheet: -0.52 (0.91), residues: 37 loop : -0.04 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 472 TYR 0.021 0.001 TYR H 68 PHE 0.026 0.001 PHE B 246 TRP 0.013 0.001 TRP A 131 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (18838) covalent geometry : angle 0.92256 / 0.36 (26148) hydrogen bonds : bond 0.04699 / 3.16 ( 897) hydrogen bonds : angle 4.58738 / 3.41 ( 2577) Misc. bond : bond 0.02317 / 1.58 ( 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: 17 poor density : 117 time to evaluate : 0.439 Fit side-chains REVERT: A 59 ASP cc_start: 0.8853 (p0) cc_final: 0.8534 (p0) REVERT: A 104 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8766 (tm-30) REVERT: D 225 ASP cc_start: 0.6754 (t70) cc_final: 0.6166 (p0) REVERT: E 17 ILE cc_start: 0.7773 (mm) cc_final: 0.7473 (tp) REVERT: E 62 GLU cc_start: 0.8590 (mp0) cc_final: 0.8147 (pm20) REVERT: E 77 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8168 (tmtt) REVERT: H 36 GLU cc_start: 0.7724 (tt0) cc_final: 0.7095 (tp30) REVERT: H 76 ASP cc_start: 0.7632 (t70) cc_final: 0.7400 (t0) REVERT: K 24 VAL cc_start: 0.9203 (t) cc_final: 0.8975 (p) outliers start: 17 outliers final: 5 residues processed: 128 average time/residue: 0.5115 time to fit residues: 74.2455 Evaluate side-chains 112 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP 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: 0.0470 chunk 123 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 189 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN 2 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057483 restraints weight = 45848.617| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.26 r_work: 0.2738 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 18872 Z= 0.139 Angle : 0.880 44.322 26148 Z= 0.343 Chirality : 0.040 0.248 2517 Planarity : 0.004 0.057 3302 Dihedral : 15.107 169.580 3212 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.77 % Allowed : 10.49 % Favored : 88.74 % 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 are not related in a simple way. whole: 1.74 (0.20), residues: 1897 helix: 1.95 (0.15), residues: 1150 sheet: -0.55 (0.89), residues: 37 loop : -0.02 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 345 TYR 0.015 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 C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (18838) covalent geometry : angle 0.88029 / 0.34 (26148) hydrogen bonds : bond 0.04225 / 2.85 ( 897) hydrogen bonds : angle 4.43803 / 3.29 ( 2577) Misc. bond : bond 0.01812 / 1.42 ( 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 133 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8751 (p0) cc_final: 0.8493 (p0) REVERT: A 104 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8773 (tm-30) REVERT: B 60 MET cc_start: 0.9533 (mmp) cc_final: 0.8971 (mmp) REVERT: D 225 ASP cc_start: 0.6816 (t70) cc_final: 0.6249 (p0) REVERT: E 8 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7761 (ttt180) REVERT: E 17 ILE cc_start: 0.7907 (mm) cc_final: 0.7643 (tp) REVERT: E 24 SER cc_start: 0.8654 (m) cc_final: 0.8172 (p) REVERT: E 62 GLU cc_start: 0.8653 (mp0) cc_final: 0.8116 (pm20) REVERT: E 77 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8194 (tmtt) REVERT: H 36 GLU cc_start: 0.7694 (tt0) cc_final: 0.7122 (tp30) REVERT: H 76 ASP cc_start: 0.7659 (t70) cc_final: 0.7436 (t0) REVERT: K 24 VAL cc_start: 0.9212 (t) cc_final: 0.8984 (p) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.5472 time to fit residues: 78.9965 Evaluate side-chains 121 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 H residue 75 ASP 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: 7.9990 chunk 145 optimal weight: 0.2980 chunk 86 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3306 r_free = 0.3306 target = 0.076414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.056144 restraints weight = 45972.914| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.26 r_work: 0.2712 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1579 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= 0.168 Angle : 0.884 44.439 26148 Z= 0.347 Chirality : 0.041 0.260 2517 Planarity : 0.004 0.056 3302 Dihedral : 14.526 170.067 3212 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.42 % Allowed : 10.75 % Favored : 87.84 % 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 are not related in a simple way. whole: 1.74 (0.19), residues: 1897 helix: 1.97 (0.15), residues: 1138 sheet: -0.56 (0.89), residues: 37 loop : -0.02 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 345 TYR 0.017 0.001 TYR H 68 PHE 0.024 0.001 PHE B 246 TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (18838) covalent geometry : angle 0.88357 / 0.35 (26148) hydrogen bonds : bond 0.04414 / 2.98 ( 897) hydrogen bonds : angle 4.45133 / 3.31 ( 2577) Misc. bond : bond 0.02301 / 1.61 ( 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 141 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8787 (p0) cc_final: 0.8539 (p0) REVERT: A 104 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8723 (tm-30) REVERT: C 402 ILE cc_start: 0.2375 (OUTLIER) cc_final: 0.2111 (pp) REVERT: D 225 ASP cc_start: 0.6863 (t70) cc_final: 0.6298 (p0) REVERT: E 8 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.7771 (ttt180) REVERT: E 17 ILE cc_start: 0.7967 (mm) cc_final: 0.7710 (tp) REVERT: E 24 SER cc_start: 0.8700 (m) cc_final: 0.8239 (p) REVERT: E 77 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8183 (tmtt) REVERT: H 36 GLU cc_start: 0.7818 (tt0) cc_final: 0.7268 (tp30) REVERT: K 24 VAL cc_start: 0.9231 (t) cc_final: 0.9019 (p) outliers start: 22 outliers final: 10 residues processed: 136 average time/residue: 0.5500 time to fit residues: 84.8874 Evaluate side-chains 124 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 91 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3319 r_free = 0.3319 target = 0.076964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.057115 restraints weight = 45442.149| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.25 r_work: 0.2732 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1621 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 : 0.866 44.354 26148 Z= 0.339 Chirality : 0.040 0.257 2517 Planarity : 0.004 0.055 3302 Dihedral : 14.207 170.931 3212 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.84 % Allowed : 12.23 % Favored : 86.94 % 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 are not related in a simple way. whole: 1.78 (0.19), residues: 1897 helix: 2.02 (0.15), residues: 1138 sheet: -0.58 (0.89), 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 0.013 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 C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (18838) covalent geometry : angle 0.86609 / 0.34 (26148) hydrogen bonds : bond 0.04184 / 2.83 ( 897) hydrogen bonds : angle 4.37398 / 3.25 ( 2577) Misc. bond : bond 0.02057 / 1.53 ( 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 132 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8722 (p0) cc_final: 0.8486 (p0) REVERT: A 104 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8744 (tm-30) REVERT: C 402 ILE cc_start: 0.2354 (OUTLIER) cc_final: 0.2098 (pp) REVERT: D 225 ASP cc_start: 0.6849 (t70) cc_final: 0.6296 (p0) REVERT: E 8 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7703 (ttt180) REVERT: E 17 ILE cc_start: 0.7954 (mm) cc_final: 0.7705 (tp) REVERT: E 24 SER cc_start: 0.8731 (m) cc_final: 0.8297 (p) REVERT: E 62 GLU cc_start: 0.8504 (mp0) cc_final: 0.7999 (pm20) REVERT: E 77 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8170 (tmtt) REVERT: H 36 GLU cc_start: 0.7850 (tt0) cc_final: 0.7575 (tt0) REVERT: K 24 VAL cc_start: 0.9218 (t) cc_final: 0.9013 (p) outliers start: 13 outliers final: 7 residues processed: 127 average time/residue: 0.5680 time to fit residues: 81.4707 Evaluate side-chains 121 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 277 MET Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 345 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 42 optimal weight: 0.0770 chunk 85 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 10 optimal weight: 0.0170 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3357 r_free = 0.3357 target = 0.078882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059217 restraints weight = 45457.999| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.26 r_work: 0.2785 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.100 18872 Z= 0.106 Angle : 0.851 44.231 26148 Z= 0.331 Chirality : 0.039 0.242 2517 Planarity : 0.004 0.054 3302 Dihedral : 13.837 175.177 3212 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.09 % Allowed : 12.68 % Favored : 86.23 % 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 are not related in a simple way. whole: 1.90 (0.20), residues: 1897 helix: 2.14 (0.15), residues: 1140 sheet: -0.87 (0.82), residues: 42 loop : -0.00 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 345 TYR 0.010 0.001 TYR D 244 PHE 0.018 0.001 PHE B 246 TRP 0.014 0.001 TRP C 51 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (18838) covalent geometry : angle 0.85058 / 0.33 (26148) hydrogen bonds : bond 0.03787 / 2.58 ( 897) hydrogen bonds : angle 4.21725 / 3.14 ( 2577) Misc. bond : bond 0.01732 / 1.47 ( 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 136 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8549 (p0) cc_final: 0.8343 (p0) REVERT: A 104 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8754 (tm-30) REVERT: C 402 ILE cc_start: 0.2539 (OUTLIER) cc_final: 0.2292 (pp) REVERT: D 225 ASP cc_start: 0.6966 (t70) cc_final: 0.6397 (p0) REVERT: E 8 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7820 (ttt180) REVERT: E 17 ILE cc_start: 0.7942 (mm) cc_final: 0.7713 (tp) REVERT: E 18 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7173 (ppt170) REVERT: E 24 SER cc_start: 0.8750 (m) cc_final: 0.8326 (p) REVERT: E 62 GLU cc_start: 0.8585 (mp0) cc_final: 0.8067 (pm20) REVERT: E 77 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8214 (tmtt) REVERT: H 36 GLU cc_start: 0.7810 (tt0) cc_final: 0.7529 (tt0) REVERT: K 24 VAL cc_start: 0.9174 (t) cc_final: 0.8965 (p) REVERT: 2 129 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7101 (mp) outliers start: 17 outliers final: 12 residues processed: 133 average time/residue: 0.5263 time to fit residues: 79.5231 Evaluate side-chains 129 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 277 MET 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 75 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3333 r_free = 0.3333 target = 0.077805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.057753 restraints weight = 45369.006| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.27 r_work: 0.2750 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1752 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= 0.132 Angle : 0.861 44.329 26148 Z= 0.337 Chirality : 0.040 0.289 2517 Planarity : 0.004 0.055 3302 Dihedral : 13.823 174.520 3212 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.29 % Allowed : 13.06 % Favored : 85.65 % 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 are not related in a simple way. whole: 1.88 (0.20), residues: 1897 helix: 2.12 (0.15), residues: 1140 sheet: -0.50 (0.90), residues: 37 loop : -0.02 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.012 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 C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (18838) covalent geometry : angle 0.86125 / 0.34 (26148) hydrogen bonds : bond 0.03985 / 2.71 ( 897) hydrogen bonds : angle 4.23846 / 3.16 ( 2577) Misc. bond : bond 0.02060 / 1.57 ( 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 136 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8624 (p0) cc_final: 0.8422 (p0) REVERT: A 104 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8733 (tm-30) REVERT: C 402 ILE cc_start: 0.2532 (OUTLIER) cc_final: 0.2281 (pp) REVERT: D 225 ASP cc_start: 0.6970 (t70) cc_final: 0.6397 (p0) REVERT: E 8 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7763 (ttt180) REVERT: E 17 ILE cc_start: 0.7979 (mm) cc_final: 0.7747 (tp) REVERT: E 18 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7227 (ppt170) REVERT: E 24 SER cc_start: 0.8765 (m) cc_final: 0.8348 (p) REVERT: E 62 GLU cc_start: 0.8604 (mp0) cc_final: 0.8083 (pm20) REVERT: E 77 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8264 (tmtt) REVERT: H 36 GLU cc_start: 0.7862 (tt0) cc_final: 0.7627 (tt0) REVERT: H 77 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.6957 (t) REVERT: K 24 VAL cc_start: 0.9191 (t) cc_final: 0.8979 (p) REVERT: 2 95 ASN cc_start: 0.6553 (t0) cc_final: 0.6263 (t0) outliers start: 20 outliers final: 11 residues processed: 130 average time/residue: 0.5587 time to fit residues: 82.3797 Evaluate side-chains 128 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 75 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 13 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 103 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 5 optimal weight: 0.0980 chunk 149 optimal weight: 0.0970 chunk 145 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3346 r_free = 0.3346 target = 0.078387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.058387 restraints weight = 45554.036| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.26 r_work: 0.2768 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 18872 Z= 0.114 Angle : 0.858 44.290 26148 Z= 0.337 Chirality : 0.040 0.294 2517 Planarity : 0.004 0.055 3302 Dihedral : 13.706 175.025 3212 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.29 % Allowed : 13.19 % Favored : 85.52 % 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 are not related in a simple way. whole: 1.91 (0.20), residues: 1897 helix: 2.15 (0.15), residues: 1138 sheet: -0.47 (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 0.021 0.001 PHE B 246 TRP 0.013 0.001 TRP C 51 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (18838) covalent geometry : angle 0.85760 / 0.34 (26148) hydrogen bonds : bond 0.03868 / 2.63 ( 897) hydrogen bonds : angle 4.20030 / 3.13 ( 2577) Misc. bond : bond 0.01880 / 1.52 ( 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 139 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8585 (p0) cc_final: 0.8367 (p0) REVERT: A 104 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8683 (tm-30) REVERT: C 402 ILE cc_start: 0.2535 (OUTLIER) cc_final: 0.2289 (pp) REVERT: D 225 ASP cc_start: 0.7031 (t70) cc_final: 0.6481 (p0) REVERT: E 8 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7812 (ttt180) REVERT: E 17 ILE cc_start: 0.7938 (mm) cc_final: 0.7717 (tp) REVERT: E 18 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7230 (ppt170) REVERT: E 24 SER cc_start: 0.8724 (m) cc_final: 0.8310 (p) REVERT: E 62 GLU cc_start: 0.8570 (mp0) cc_final: 0.8027 (pm20) REVERT: E 77 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8195 (tmtt) REVERT: H 36 GLU cc_start: 0.7755 (tt0) cc_final: 0.7449 (tt0) REVERT: K 24 VAL cc_start: 0.9175 (t) cc_final: 0.8961 (p) REVERT: 2 95 ASN cc_start: 0.6528 (t0) cc_final: 0.6250 (t0) outliers start: 20 outliers final: 12 residues processed: 133 average time/residue: 0.5111 time to fit residues: 77.1468 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 : 0.472 ------------------------------------------------------------------------------- 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 61 VAL 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: 2.9990 chunk 165 optimal weight: 8.9990 chunk 169 optimal weight: 0.4980 chunk 173 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3333 r_free = 0.3333 target = 0.077688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057973 restraints weight = 45367.667| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.26 r_work: 0.2753 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1835 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= 0.134 Angle : 0.862 44.365 26148 Z= 0.339 Chirality : 0.040 0.295 2517 Planarity : 0.004 0.055 3302 Dihedral : 13.669 174.788 3212 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.16 % Allowed : 13.32 % Favored : 85.52 % 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 are not related in a simple way. whole: 1.89 (0.20), residues: 1897 helix: 2.12 (0.15), residues: 1135 sheet: -0.26 (0.94), residues: 35 loop : -0.01 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.012 0.001 TYR H 68 PHE 0.022 0.001 PHE B 246 TRP 0.012 0.001 TRP A 131 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (18838) covalent geometry : angle 0.86245 / 0.34 (26148) hydrogen bonds : bond 0.04034 / 2.74 ( 897) hydrogen bonds : angle 4.23052 / 3.15 ( 2577) Misc. bond : bond 0.02092 / 1.57 ( 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 133 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8645 (p0) cc_final: 0.8409 (p0) REVERT: A 104 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8722 (tm-30) REVERT: C 402 ILE cc_start: 0.2472 (OUTLIER) cc_final: 0.2232 (pp) REVERT: E 8 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7785 (ttt180) REVERT: E 17 ILE cc_start: 0.7979 (mm) cc_final: 0.7756 (tp) REVERT: E 18 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7251 (ppt170) REVERT: E 62 GLU cc_start: 0.8579 (mp0) cc_final: 0.8022 (pm20) REVERT: E 77 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8214 (tmtt) REVERT: H 36 GLU cc_start: 0.7797 (tt0) cc_final: 0.7553 (tt0) REVERT: K 24 VAL cc_start: 0.9186 (t) cc_final: 0.8966 (p) REVERT: 2 95 ASN cc_start: 0.6532 (t0) cc_final: 0.6311 (t0) outliers start: 18 outliers final: 13 residues processed: 130 average time/residue: 0.5394 time to fit residues: 79.8406 Evaluate side-chains 139 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 277 MET 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 61 VAL 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 109 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 59 optimal weight: 0.0170 chunk 155 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3353 r_free = 0.3353 target = 0.078731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058860 restraints weight = 45424.536| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.27 r_work: 0.2779 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 18872 Z= 0.110 Angle : 0.861 44.275 26148 Z= 0.337 Chirality : 0.040 0.421 2517 Planarity : 0.004 0.054 3302 Dihedral : 13.521 176.574 3212 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.16 % Allowed : 13.45 % 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 are not related in a simple way. whole: 1.94 (0.20), residues: 1897 helix: 2.18 (0.15), residues: 1135 sheet: -0.82 (0.82), residues: 42 loop : 0.03 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 117 TYR 0.010 0.001 TYR H 68 PHE 0.020 0.001 PHE B 246 TRP 0.013 0.001 TRP C 51 HIS 0.003 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (18838) covalent geometry : angle 0.86086 / 0.34 (26148) hydrogen bonds : bond 0.03785 / 2.58 ( 897) hydrogen bonds : angle 4.17311 / 3.10 ( 2577) Misc. bond : bond 0.01760 / 1.49 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5126.03 seconds wall clock time: 88 minutes 16.67 seconds (5296.67 seconds total)