Starting phenix.real_space_refine on Thu Jan 23 17:02:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2i_18848/01_2025/8r2i_18848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2i_18848/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r2i_18848/01_2025/8r2i_18848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2i_18848/01_2025/8r2i_18848.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2i_18848/01_2025/8r2i_18848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2i_18848/01_2025/8r2i_18848.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 11.02, per 1000 atoms: 0.61 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: 6.04 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.60 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: 5.45 Time building geometry restraints manager: 6.69 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: 2.330 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.200 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.460 ------------------------------------------------------------------------------- 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 : 0.021 0.264 18838 Z= 1.146 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 : 12.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (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 TRP 0.015 0.001 TRP A 131 HIS 0.007 0.001 HIS B 466 PHE 0.039 0.001 PHE D 185 TYR 0.016 0.001 TYR H 68 ARG 0.004 0.000 ARG E 8 *********************** 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 : 1.922 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 1.3657 time to fit residues: 254.9877 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 : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3326 r_free = 0.3326 target = 0.077417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.056934 restraints weight = 45458.977| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.27 r_work: 0.2742 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18838 Z= 0.271 Angle : 0.942 44.406 26148 Z= 0.370 Chirality : 0.044 0.335 2517 Planarity : 0.005 0.057 3296 Dihedral : 21.101 166.377 3212 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.77 % Allowed : 7.98 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1897 helix: 1.93 (0.15), residues: 1135 sheet: -0.53 (0.90), residues: 37 loop : -0.07 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.004 0.001 HIS C 418 PHE 0.028 0.001 PHE B 246 TYR 0.010 0.001 TYR E 44 ARG 0.003 0.000 ARG C 345 *********************** 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 131 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.772 Fit side-chains REVERT: A 104 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8662 (tm-30) REVERT: B 55 MET cc_start: 0.9350 (ptp) cc_final: 0.9120 (ptm) REVERT: D 225 ASP cc_start: 0.6721 (t70) cc_final: 0.6118 (p0) REVERT: E 24 SER cc_start: 0.8750 (m) cc_final: 0.8310 (p) REVERT: E 71 ASN cc_start: 0.8836 (m110) cc_final: 0.8625 (t0) REVERT: E 77 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8218 (tmtt) REVERT: H 36 GLU cc_start: 0.7511 (tt0) cc_final: 0.6990 (tp30) REVERT: K 10 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8225 (mmpt) REVERT: K 24 VAL cc_start: 0.9191 (t) cc_final: 0.8959 (p) outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 1.2963 time to fit residues: 181.5616 Evaluate side-chains 117 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain K residue 10 LYS 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 16 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 67 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 73 optimal weight: 0.0040 chunk 122 optimal weight: 0.0060 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 GLN 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 = 0.3363 r_free = 0.3363 target = 0.079748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.059373 restraints weight = 45166.302| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.27 r_work: 0.2787 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18838 Z= 0.145 Angle : 0.888 44.206 26148 Z= 0.343 Chirality : 0.041 0.335 2517 Planarity : 0.004 0.056 3296 Dihedral : 17.350 169.006 3212 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.77 % Allowed : 8.94 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1897 helix: 2.04 (0.15), residues: 1146 sheet: -0.82 (0.82), residues: 42 loop : 0.01 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 51 HIS 0.004 0.001 HIS D 268 PHE 0.021 0.001 PHE B 246 TYR 0.009 0.001 TYR D 244 ARG 0.002 0.000 ARG A 269 *********************** 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 136 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.671 Fit side-chains REVERT: A 59 ASP cc_start: 0.8660 (p0) cc_final: 0.8357 (p0) REVERT: A 104 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8737 (tm-30) REVERT: B 55 MET cc_start: 0.9321 (ptp) cc_final: 0.9087 (ptm) REVERT: D 225 ASP cc_start: 0.6769 (t70) cc_final: 0.6202 (p0) REVERT: E 8 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7734 (ttt180) REVERT: E 17 ILE cc_start: 0.7804 (mm) cc_final: 0.7511 (tp) REVERT: E 24 SER cc_start: 0.8684 (m) cc_final: 0.8256 (p) REVERT: E 62 GLU cc_start: 0.8564 (mp0) cc_final: 0.8146 (pm20) REVERT: E 77 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8174 (tmtt) REVERT: H 36 GLU cc_start: 0.7503 (tt0) cc_final: 0.6905 (tp30) REVERT: H 76 ASP cc_start: 0.7542 (t70) cc_final: 0.7281 (t0) REVERT: H 79 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6532 (tmm) REVERT: K 24 VAL cc_start: 0.9187 (t) cc_final: 0.8954 (p) outliers start: 12 outliers final: 4 residues processed: 130 average time/residue: 1.2584 time to fit residues: 186.3209 Evaluate side-chains 116 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 14 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 136 optimal weight: 4.9990 chunk 112 optimal weight: 0.0770 chunk 105 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 168 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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** 2 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.059039 restraints weight = 45676.446| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.28 r_work: 0.2779 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18838 Z= 0.156 Angle : 0.868 44.177 26148 Z= 0.336 Chirality : 0.040 0.313 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.925 169.585 3212 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.84 % Allowed : 10.17 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.20), residues: 1897 helix: 2.05 (0.15), residues: 1147 sheet: -0.52 (0.89), residues: 37 loop : -0.02 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 131 HIS 0.003 0.001 HIS C 225 PHE 0.020 0.001 PHE B 246 TYR 0.008 0.001 TYR B 172 ARG 0.002 0.000 ARG C 345 *********************** 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 134 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8649 (p0) cc_final: 0.8355 (p0) REVERT: A 104 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8772 (tm-30) REVERT: B 55 MET cc_start: 0.9314 (ptp) cc_final: 0.9106 (ptm) REVERT: D 225 ASP cc_start: 0.6798 (t70) cc_final: 0.6253 (p0) REVERT: E 8 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.7757 (ttt180) REVERT: E 17 ILE cc_start: 0.7828 (mm) cc_final: 0.7560 (tp) REVERT: E 62 GLU cc_start: 0.8649 (mp0) cc_final: 0.8216 (pm20) REVERT: E 77 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8191 (tmtt) REVERT: H 36 GLU cc_start: 0.7584 (tt0) cc_final: 0.6994 (tp30) REVERT: K 24 VAL cc_start: 0.9209 (t) cc_final: 0.8984 (p) REVERT: 2 45 LYS cc_start: 0.8557 (mmmm) cc_final: 0.8326 (mttp) REVERT: 2 129 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6883 (mp) outliers start: 13 outliers final: 7 residues processed: 127 average time/residue: 1.2938 time to fit residues: 186.7020 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 : 1.745 ------------------------------------------------------------------------------- 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 277 MET 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 2 residue 129 LEU 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 78 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** 2 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.078581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.058482 restraints weight = 45936.856| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.27 r_work: 0.2768 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18838 Z= 0.172 Angle : 0.855 44.232 26148 Z= 0.332 Chirality : 0.040 0.324 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.329 170.077 3212 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.90 % Allowed : 10.94 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.20), residues: 1897 helix: 2.07 (0.15), residues: 1149 sheet: -0.46 (0.89), residues: 37 loop : -0.04 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 51 HIS 0.003 0.001 HIS F 23 PHE 0.022 0.001 PHE B 246 TYR 0.008 0.001 TYR H 68 ARG 0.003 0.000 ARG B 177 *********************** 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 129 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8667 (p0) cc_final: 0.8370 (p0) REVERT: A 104 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8725 (tm-30) REVERT: B 60 MET cc_start: 0.9483 (mmp) cc_final: 0.8958 (mmp) REVERT: C 402 ILE cc_start: 0.2231 (OUTLIER) cc_final: 0.1978 (pp) REVERT: D 225 ASP cc_start: 0.6886 (t70) cc_final: 0.6290 (p0) REVERT: E 8 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7785 (ttt180) REVERT: E 17 ILE cc_start: 0.7890 (mm) cc_final: 0.7621 (tp) REVERT: E 24 SER cc_start: 0.8651 (m) cc_final: 0.8186 (p) REVERT: E 77 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8185 (tmtt) REVERT: H 36 GLU cc_start: 0.7650 (tt0) cc_final: 0.7040 (tp30) REVERT: K 24 VAL cc_start: 0.9174 (t) cc_final: 0.8939 (p) REVERT: 2 129 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6863 (mp) outliers start: 14 outliers final: 8 residues processed: 124 average time/residue: 1.2961 time to fit residues: 181.9794 Evaluate side-chains 118 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 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 2 residue 50 LEU Chi-restraints excluded: chain 2 residue 129 LEU 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 140 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.076778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056413 restraints weight = 46180.929| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.28 r_work: 0.2719 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18838 Z= 0.263 Angle : 0.881 44.406 26148 Z= 0.347 Chirality : 0.042 0.344 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.314 169.634 3212 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.97 % Allowed : 12.03 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1897 helix: 2.04 (0.15), residues: 1138 sheet: -0.53 (0.90), residues: 37 loop : 0.01 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 131 HIS 0.004 0.001 HIS B 114 PHE 0.024 0.001 PHE B 246 TYR 0.011 0.001 TYR H 68 ARG 0.003 0.000 ARG C 345 *********************** 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 129 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.858 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8773 (p0) cc_final: 0.8485 (p0) REVERT: A 104 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8785 (tm-30) REVERT: D 225 ASP cc_start: 0.6892 (t70) cc_final: 0.6346 (p0) REVERT: E 8 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.7743 (ttt180) REVERT: E 17 ILE cc_start: 0.8011 (mm) cc_final: 0.7761 (tp) REVERT: E 24 SER cc_start: 0.8734 (m) cc_final: 0.8273 (p) REVERT: E 62 GLU cc_start: 0.8640 (mp0) cc_final: 0.8241 (pm20) REVERT: E 77 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8206 (tmtt) REVERT: H 36 GLU cc_start: 0.7812 (tt0) cc_final: 0.7267 (tp30) REVERT: K 24 VAL cc_start: 0.9200 (t) cc_final: 0.8975 (p) REVERT: 2 129 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6900 (mp) outliers start: 15 outliers final: 7 residues processed: 124 average time/residue: 1.2979 time to fit residues: 183.2154 Evaluate side-chains 118 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 F residue 20 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 2 residue 129 LEU 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 30 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 172 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.078547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.058506 restraints weight = 45435.277| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.27 r_work: 0.2768 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18838 Z= 0.153 Angle : 0.855 44.206 26148 Z= 0.334 Chirality : 0.040 0.386 2517 Planarity : 0.004 0.054 3296 Dihedral : 15.046 171.572 3212 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.03 % Allowed : 12.36 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.20), residues: 1897 helix: 2.10 (0.15), residues: 1141 sheet: -0.53 (0.89), residues: 37 loop : -0.01 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 51 HIS 0.003 0.001 HIS C 418 PHE 0.020 0.001 PHE B 246 TYR 0.008 0.001 TYR C 259 ARG 0.001 0.000 ARG B 7 *********************** 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: 16 poor density : 120 time to evaluate : 1.827 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8624 (p0) cc_final: 0.8371 (p0) REVERT: A 104 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8779 (tm-30) REVERT: C 402 ILE cc_start: 0.2420 (OUTLIER) cc_final: 0.2173 (pp) REVERT: D 225 ASP cc_start: 0.6839 (t70) cc_final: 0.6306 (p0) REVERT: E 8 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7846 (ttt180) REVERT: E 17 ILE cc_start: 0.7973 (mm) cc_final: 0.7735 (tp) REVERT: E 24 SER cc_start: 0.8719 (m) cc_final: 0.8244 (p) REVERT: E 62 GLU cc_start: 0.8666 (mp0) cc_final: 0.8254 (pm20) REVERT: E 77 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8221 (tmtt) REVERT: H 36 GLU cc_start: 0.7812 (tt0) cc_final: 0.7543 (tt0) REVERT: K 24 VAL cc_start: 0.9203 (t) cc_final: 0.8985 (p) REVERT: 2 45 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8324 (mttp) outliers start: 16 outliers final: 10 residues processed: 131 average time/residue: 1.3437 time to fit residues: 199.8347 Evaluate side-chains 125 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 185 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.077051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056839 restraints weight = 45679.067| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.27 r_work: 0.2729 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18838 Z= 0.227 Angle : 0.874 44.387 26148 Z= 0.343 Chirality : 0.042 0.375 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.073 171.967 3212 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.09 % Allowed : 12.61 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 1897 helix: 2.04 (0.15), residues: 1135 sheet: -0.34 (0.94), residues: 35 loop : 0.00 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 131 HIS 0.004 0.001 HIS B 114 PHE 0.023 0.001 PHE B 246 TYR 0.010 0.001 TYR H 68 ARG 0.003 0.000 ARG E 18 *********************** 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 132 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8725 (p0) cc_final: 0.8448 (p0) REVERT: A 104 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8718 (tm-30) REVERT: B 60 MET cc_start: 0.9528 (mmp) cc_final: 0.8830 (mmp) REVERT: C 402 ILE cc_start: 0.2479 (OUTLIER) cc_final: 0.2229 (pp) REVERT: D 225 ASP cc_start: 0.6867 (t70) cc_final: 0.6326 (p0) REVERT: E 8 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7665 (ttt180) REVERT: E 17 ILE cc_start: 0.7925 (mm) cc_final: 0.7669 (tp) REVERT: E 24 SER cc_start: 0.8692 (m) cc_final: 0.8231 (p) REVERT: E 62 GLU cc_start: 0.8636 (mp0) cc_final: 0.8177 (pm20) REVERT: E 77 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8171 (tmtt) REVERT: H 36 GLU cc_start: 0.7869 (tt0) cc_final: 0.7597 (tt0) REVERT: K 24 VAL cc_start: 0.9184 (t) cc_final: 0.8970 (p) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 1.2436 time to fit residues: 178.6952 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 : 1.843 ------------------------------------------------------------------------------- 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 340 VAL 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 2 residue 61 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 61 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 = 0.3278 r_free = 0.3278 target = 0.074981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054876 restraints weight = 46623.088| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.26 r_work: 0.2675 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18838 Z= 0.343 Angle : 0.926 44.655 26148 Z= 0.373 Chirality : 0.045 0.411 2517 Planarity : 0.005 0.056 3296 Dihedral : 15.387 168.521 3212 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.97 % Allowed : 13.06 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 1897 helix: 1.88 (0.15), residues: 1132 sheet: -0.34 (0.94), residues: 35 loop : -0.06 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.005 0.001 HIS B 114 PHE 0.024 0.002 PHE B 246 TYR 0.013 0.001 TYR H 68 ARG 0.004 0.000 ARG E 18 *********************** 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 132 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8864 (p0) cc_final: 0.8601 (p0) REVERT: A 104 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8757 (tm-30) REVERT: C 402 ILE cc_start: 0.2452 (OUTLIER) cc_final: 0.2185 (pp) REVERT: D 225 ASP cc_start: 0.6794 (t70) cc_final: 0.6290 (p0) REVERT: E 8 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7729 (ttt180) REVERT: E 17 ILE cc_start: 0.7966 (mm) cc_final: 0.7730 (tp) REVERT: E 62 GLU cc_start: 0.8635 (mp0) cc_final: 0.8164 (pm20) REVERT: E 77 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8135 (tmtt) outliers start: 15 outliers final: 13 residues processed: 127 average time/residue: 1.3746 time to fit residues: 198.7975 Evaluate side-chains 125 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 246 PHE 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 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 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 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 87 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.076905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.056849 restraints weight = 45748.837| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.27 r_work: 0.2728 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18838 Z= 0.171 Angle : 0.882 44.286 26148 Z= 0.349 Chirality : 0.041 0.407 2517 Planarity : 0.004 0.054 3296 Dihedral : 15.132 170.848 3212 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.97 % Allowed : 13.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 1897 helix: 1.99 (0.15), residues: 1135 sheet: -0.38 (0.92), residues: 35 loop : -0.04 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 51 HIS 0.004 0.001 HIS C 418 PHE 0.023 0.001 PHE B 246 TYR 0.011 0.001 TYR C 259 ARG 0.003 0.000 ARG E 18 ********************** 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 130 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 2.086 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8747 (p0) cc_final: 0.8511 (p0) REVERT: A 104 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8748 (tm-30) REVERT: C 402 ILE cc_start: 0.2583 (OUTLIER) cc_final: 0.2329 (pp) REVERT: E 8 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7708 (ttt180) REVERT: E 17 ILE cc_start: 0.7959 (mm) cc_final: 0.7722 (tp) REVERT: E 24 SER cc_start: 0.8695 (t) cc_final: 0.7887 (p) REVERT: E 62 GLU cc_start: 0.8625 (mp0) cc_final: 0.8157 (pm20) REVERT: E 77 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8135 (tmtt) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 1.3074 time to fit residues: 184.9223 Evaluate side-chains 122 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 246 PHE 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 340 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 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 87 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 160 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.078298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.058356 restraints weight = 45392.778| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.26 r_work: 0.2770 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 : 0.002 0.038 18838 Z= 0.154 Angle : 0.866 44.293 26148 Z= 0.340 Chirality : 0.040 0.406 2517 Planarity : 0.004 0.054 3296 Dihedral : 14.846 175.626 3212 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.77 % Allowed : 13.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1897 helix: 2.09 (0.15), residues: 1136 sheet: -0.27 (0.92), residues: 35 loop : -0.05 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 131 HIS 0.005 0.001 HIS A 195 PHE 0.017 0.001 PHE B 246 TYR 0.009 0.001 TYR C 259 ARG 0.003 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10397.76 seconds wall clock time: 185 minutes 14.17 seconds (11114.17 seconds total)