Starting phenix.real_space_refine on Tue Jun 17 23:26:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r2i_18848/06_2025/8r2i_18848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r2i_18848/06_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_18848/06_2025/8r2i_18848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r2i_18848/06_2025/8r2i_18848.map" model { file = "/net/cci-nas-00/data/ceres_data/8r2i_18848/06_2025/8r2i_18848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r2i_18848/06_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): 1.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.45, per 1000 atoms: 0.63 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: 6.68 Conformation dependent library (CDL) restraints added in 2.3 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: 1.72 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: 5.41 Time building geometry restraints manager: 7.55 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: 0.010 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 44.730 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 0.686 18872 Z= 1.876 Angle : 1.619 47.403 26148 Z= 0.573 Chirality : 0.088 0.769 2517 Planarity : 0.008 0.112 3296 Dihedral : 21.202 162.774 6452 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 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 Details of bonding type rmsd hydrogen bonds : bond 0.11816 ( 897) hydrogen bonds : angle 5.69481 ( 2577) covalent geometry : bond 0.02117 (18838) covalent geometry : angle 1.61908 (26148) Misc. bond : bond 0.37142 ( 34) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.502 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 1.3678 time to fit residues: 256.9551 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 : 1.901 ------------------------------------------------------------------------------- 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: 20.0000 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 = 0.077359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.057015 restraints weight = 45439.817| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.28 r_work: 0.2741 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 18872 Z= 0.186 Angle : 0.942 44.404 26148 Z= 0.370 Chirality : 0.044 0.336 2517 Planarity : 0.005 0.057 3296 Dihedral : 21.097 166.383 3212 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.68 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 Details of bonding type rmsd hydrogen bonds : bond 0.04866 ( 897) hydrogen bonds : angle 4.76111 ( 2577) covalent geometry : bond 0.00424 (18838) covalent geometry : angle 0.94205 (26148) Misc. bond : bond 0.01859 ( 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 131 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 3.192 Fit side-chains REVERT: A 104 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8666 (tm-30) REVERT: B 55 MET cc_start: 0.9347 (ptp) cc_final: 0.9119 (ptm) REVERT: D 225 ASP cc_start: 0.6712 (t70) cc_final: 0.6111 (p0) REVERT: E 24 SER cc_start: 0.8746 (m) cc_final: 0.8306 (p) REVERT: E 71 ASN cc_start: 0.8836 (m110) cc_final: 0.8624 (t0) REVERT: E 77 LYS cc_start: 0.8526 (ttpt) cc_final: 0.8198 (tmtt) REVERT: H 36 GLU cc_start: 0.7511 (tt0) cc_final: 0.6989 (tp30) REVERT: K 10 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8218 (mmpt) REVERT: K 24 VAL cc_start: 0.9187 (t) cc_final: 0.8954 (p) outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 1.8115 time to fit residues: 251.2551 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 : 2.514 ------------------------------------------------------------------------------- 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: 3.9990 chunk 138 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.077986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.057637 restraints weight = 45375.074| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.27 r_work: 0.2746 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1293 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= 0.136 Angle : 0.897 44.297 26148 Z= 0.348 Chirality : 0.042 0.369 2517 Planarity : 0.004 0.055 3296 Dihedral : 17.556 169.006 3212 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.84 % Allowed : 9.14 % Favored : 90.03 % 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: 1.72 (0.20), residues: 1897 helix: 1.95 (0.15), residues: 1151 sheet: -0.50 (0.91), residues: 37 loop : -0.06 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.004 0.001 HIS C 418 PHE 0.023 0.001 PHE B 246 TYR 0.009 0.001 TYR E 44 ARG 0.002 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 897) hydrogen bonds : angle 4.49739 ( 2577) covalent geometry : bond 0.00301 (18838) covalent geometry : angle 0.89668 (26148) Misc. bond : bond 0.02110 ( 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 133 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.692 Fit side-chains REVERT: A 59 ASP cc_start: 0.8742 (p0) cc_final: 0.8482 (p0) REVERT: A 104 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8747 (tm-30) REVERT: B 60 MET cc_start: 0.9506 (mmp) cc_final: 0.8941 (mmp) REVERT: D 225 ASP cc_start: 0.6779 (t70) cc_final: 0.6201 (p0) REVERT: E 17 ILE cc_start: 0.7810 (mm) cc_final: 0.7521 (tp) REVERT: E 24 SER cc_start: 0.8726 (m) cc_final: 0.8311 (p) REVERT: E 62 GLU cc_start: 0.8585 (mp0) cc_final: 0.8205 (pm20) REVERT: E 77 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8179 (tmtt) REVERT: H 36 GLU cc_start: 0.7619 (tt0) cc_final: 0.6952 (tp30) REVERT: H 76 ASP cc_start: 0.7601 (t70) cc_final: 0.7362 (t0) REVERT: K 24 VAL cc_start: 0.9197 (t) cc_final: 0.8967 (p) outliers start: 13 outliers final: 5 residues processed: 126 average time/residue: 1.2411 time to fit residues: 179.1095 Evaluate side-chains 115 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain 1 residue 2 ASN 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: 3.9990 chunk 112 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 HIS D 189 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.055757 restraints weight = 46335.475| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.26 r_work: 0.2702 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 18872 Z= 0.206 Angle : 0.913 44.503 26148 Z= 0.360 Chirality : 0.043 0.298 2517 Planarity : 0.004 0.057 3296 Dihedral : 16.407 168.472 3212 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.03 % Allowed : 10.36 % Favored : 88.61 % 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: 1.67 (0.19), residues: 1897 helix: 1.90 (0.15), residues: 1144 sheet: -0.58 (0.90), residues: 37 loop : -0.04 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS B 114 PHE 0.025 0.001 PHE B 246 TYR 0.011 0.001 TYR H 68 ARG 0.003 0.000 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 897) hydrogen bonds : angle 4.55172 ( 2577) covalent geometry : bond 0.00477 (18838) covalent geometry : angle 0.91277 (26148) Misc. bond : bond 0.02449 ( 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: 16 poor density : 117 time to evaluate : 1.795 Fit side-chains REVERT: A 59 ASP cc_start: 0.8818 (p0) cc_final: 0.8571 (p0) REVERT: A 104 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8780 (tm-30) REVERT: D 225 ASP cc_start: 0.6798 (t70) cc_final: 0.6172 (p0) REVERT: E 17 ILE cc_start: 0.7868 (mm) cc_final: 0.7597 (tp) REVERT: E 24 SER cc_start: 0.8635 (m) cc_final: 0.8192 (p) REVERT: E 62 GLU cc_start: 0.8630 (mp0) cc_final: 0.8151 (pm20) REVERT: E 77 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8184 (tmtt) REVERT: H 36 GLU cc_start: 0.7858 (tt0) cc_final: 0.7240 (tp30) REVERT: H 76 ASP cc_start: 0.7680 (t70) cc_final: 0.7448 (t0) REVERT: K 24 VAL cc_start: 0.9256 (t) cc_final: 0.9036 (p) REVERT: 2 45 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8329 (mttp) outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 1.2250 time to fit residues: 178.1024 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 : 1.761 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 78 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.076780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.056588 restraints weight = 46280.801| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.27 r_work: 0.2727 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1590 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= 0.144 Angle : 0.877 44.362 26148 Z= 0.343 Chirality : 0.042 0.339 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.678 170.204 3212 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.22 % Allowed : 11.65 % Favored : 87.13 % 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: 1.73 (0.19), residues: 1897 helix: 1.98 (0.15), residues: 1138 sheet: -0.58 (0.88), residues: 37 loop : -0.05 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.003 0.001 HIS C 418 PHE 0.022 0.001 PHE B 246 TYR 0.010 0.001 TYR H 68 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 897) hydrogen bonds : angle 4.44403 ( 2577) covalent geometry : bond 0.00326 (18838) covalent geometry : angle 0.87657 (26148) Misc. bond : bond 0.02157 ( 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 132 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.777 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8756 (p0) cc_final: 0.8517 (p0) REVERT: A 104 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8729 (tm-30) REVERT: B 60 MET cc_start: 0.9531 (mmp) cc_final: 0.8973 (mmp) REVERT: C 402 ILE cc_start: 0.2373 (OUTLIER) cc_final: 0.2109 (pp) REVERT: D 225 ASP cc_start: 0.6831 (t70) cc_final: 0.6261 (p0) REVERT: E 8 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7692 (ttt180) REVERT: E 17 ILE cc_start: 0.7790 (mm) cc_final: 0.7583 (tt) REVERT: E 24 SER cc_start: 0.8736 (m) cc_final: 0.8321 (p) REVERT: E 62 GLU cc_start: 0.8610 (mp0) cc_final: 0.8073 (pm20) REVERT: E 77 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8126 (tmtt) REVERT: H 36 GLU cc_start: 0.7860 (tt0) cc_final: 0.7298 (tp30) REVERT: H 76 ASP cc_start: 0.7642 (t70) cc_final: 0.7416 (t0) REVERT: K 24 VAL cc_start: 0.9213 (t) cc_final: 0.9005 (p) outliers start: 19 outliers final: 11 residues processed: 128 average time/residue: 1.2540 time to fit residues: 182.2665 Evaluate side-chains 120 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 271 MET Chi-restraints excluded: chain D residue 340 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 140 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.076153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.056269 restraints weight = 46146.592| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.27 r_work: 0.2708 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1678 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= 0.169 Angle : 0.884 44.454 26148 Z= 0.349 Chirality : 0.042 0.365 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.423 170.417 3212 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.29 % Allowed : 12.48 % 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 (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: 1.70 (0.19), residues: 1897 helix: 1.95 (0.15), residues: 1138 sheet: -0.48 (0.92), residues: 35 loop : -0.07 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS B 114 PHE 0.025 0.001 PHE B 246 TYR 0.010 0.001 TYR H 68 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 897) hydrogen bonds : angle 4.45565 ( 2577) covalent geometry : bond 0.00390 (18838) covalent geometry : angle 0.88395 (26148) Misc. bond : bond 0.02403 ( 34) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8797 (p0) cc_final: 0.8538 (p0) REVERT: A 104 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8734 (tm-30) REVERT: C 402 ILE cc_start: 0.2394 (OUTLIER) cc_final: 0.2134 (pp) REVERT: D 225 ASP cc_start: 0.6845 (t70) cc_final: 0.6268 (p0) REVERT: E 8 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7734 (ttt180) REVERT: E 17 ILE cc_start: 0.7902 (mm) cc_final: 0.7674 (tt) REVERT: E 24 SER cc_start: 0.8755 (m) cc_final: 0.8328 (p) REVERT: E 77 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8136 (tmtt) REVERT: H 36 GLU cc_start: 0.7932 (tt0) cc_final: 0.7702 (tt0) REVERT: K 24 VAL cc_start: 0.9235 (t) cc_final: 0.9031 (p) outliers start: 20 outliers final: 12 residues processed: 130 average time/residue: 1.2204 time to fit residues: 181.5064 Evaluate side-chains 122 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 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 K residue 38 VAL Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 13 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 30 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.077139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.057355 restraints weight = 45629.310| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.26 r_work: 0.2738 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1706 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= 0.125 Angle : 0.868 44.357 26148 Z= 0.341 Chirality : 0.041 0.387 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.199 171.760 3212 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.48 % Allowed : 13.00 % 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 (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: 1.76 (0.19), residues: 1897 helix: 2.01 (0.15), residues: 1140 sheet: -0.46 (0.92), residues: 35 loop : -0.06 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.003 0.001 HIS C 418 PHE 0.022 0.001 PHE B 246 TYR 0.009 0.001 TYR C 259 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 897) hydrogen bonds : angle 4.36805 ( 2577) covalent geometry : bond 0.00277 (18838) covalent geometry : angle 0.86766 (26148) Misc. bond : bond 0.01923 ( 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 139 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 2.099 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8714 (p0) cc_final: 0.8483 (p0) REVERT: A 104 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8738 (tm-30) REVERT: C 391 SER cc_start: 0.5168 (OUTLIER) cc_final: 0.4967 (m) REVERT: C 402 ILE cc_start: 0.2466 (OUTLIER) cc_final: 0.2208 (pp) REVERT: D 225 ASP cc_start: 0.6906 (t70) cc_final: 0.6336 (p0) REVERT: E 8 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7757 (ttt180) REVERT: E 17 ILE cc_start: 0.7908 (mm) cc_final: 0.7663 (tp) REVERT: E 18 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7384 (ppt170) REVERT: E 24 SER cc_start: 0.8739 (m) cc_final: 0.8269 (p) REVERT: E 62 GLU cc_start: 0.8647 (mp0) cc_final: 0.8265 (pm20) REVERT: E 77 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8188 (tmtt) REVERT: H 36 GLU cc_start: 0.7890 (tt0) cc_final: 0.7594 (tt0) REVERT: K 24 VAL cc_start: 0.9228 (t) cc_final: 0.9028 (p) REVERT: 2 45 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8364 (mttp) outliers start: 23 outliers final: 11 residues processed: 132 average time/residue: 1.5962 time to fit residues: 239.1342 Evaluate side-chains 126 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 185 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.074553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.054547 restraints weight = 46446.121| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.23 r_work: 0.2667 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.213 18872 Z= 0.257 Angle : 0.939 44.764 26148 Z= 0.380 Chirality : 0.046 0.355 2517 Planarity : 0.005 0.057 3296 Dihedral : 15.584 167.835 3212 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.54 % Allowed : 13.32 % Favored : 85.14 % 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: 1.51 (0.19), residues: 1897 helix: 1.80 (0.15), residues: 1136 sheet: -0.48 (0.92), residues: 35 loop : -0.14 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.005 0.001 HIS B 114 PHE 0.025 0.002 PHE B 246 TYR 0.013 0.001 TYR H 68 ARG 0.004 0.000 ARG B 472 Details of bonding type rmsd hydrogen bonds : bond 0.05089 ( 897) hydrogen bonds : angle 4.59397 ( 2577) covalent geometry : bond 0.00600 (18838) covalent geometry : angle 0.93892 (26148) Misc. bond : bond 0.04038 ( 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 137 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8899 (p0) cc_final: 0.8638 (p0) REVERT: A 104 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8723 (tm-30) REVERT: C 391 SER cc_start: 0.5455 (OUTLIER) cc_final: 0.5213 (m) REVERT: C 402 ILE cc_start: 0.2430 (OUTLIER) cc_final: 0.2167 (pp) REVERT: D 225 ASP cc_start: 0.6813 (t70) cc_final: 0.6225 (p0) REVERT: E 17 ILE cc_start: 0.7887 (mm) cc_final: 0.7620 (tt) REVERT: E 18 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7413 (ppt170) REVERT: E 24 SER cc_start: 0.8784 (m) cc_final: 0.8368 (p) REVERT: E 62 GLU cc_start: 0.8686 (mp0) cc_final: 0.8280 (pm20) REVERT: E 77 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8227 (tmtt) outliers start: 24 outliers final: 14 residues processed: 128 average time/residue: 1.9278 time to fit residues: 280.7487 Evaluate side-chains 126 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain 1 residue 2 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 13 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 46 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.077033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057293 restraints weight = 46019.612| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.28 r_work: 0.2733 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 18872 Z= 0.125 Angle : 0.882 44.318 26148 Z= 0.349 Chirality : 0.041 0.410 2517 Planarity : 0.004 0.055 3296 Dihedral : 15.257 171.440 3212 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.42 % Allowed : 13.90 % Favored : 84.68 % 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: 1.71 (0.19), residues: 1897 helix: 2.00 (0.15), residues: 1135 sheet: -0.37 (0.93), residues: 35 loop : -0.12 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 51 HIS 0.004 0.001 HIS C 418 PHE 0.021 0.001 PHE B 246 TYR 0.009 0.001 TYR C 259 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 897) hydrogen bonds : angle 4.37518 ( 2577) covalent geometry : bond 0.00277 (18838) covalent geometry : angle 0.88210 (26148) Misc. bond : bond 0.01953 ( 34) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 2.631 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8737 (p0) cc_final: 0.8518 (p0) REVERT: A 104 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8725 (tm-30) REVERT: C 402 ILE cc_start: 0.2711 (OUTLIER) cc_final: 0.2444 (pp) REVERT: E 8 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7600 (ttt180) REVERT: E 17 ILE cc_start: 0.7911 (mm) cc_final: 0.7661 (tp) REVERT: E 18 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7323 (ppt170) REVERT: E 24 SER cc_start: 0.8747 (m) cc_final: 0.8317 (p) REVERT: E 62 GLU cc_start: 0.8633 (mp0) cc_final: 0.8219 (pm20) REVERT: E 77 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8187 (tmtt) REVERT: H 36 GLU cc_start: 0.7878 (tt0) cc_final: 0.7506 (tp30) outliers start: 22 outliers final: 9 residues processed: 132 average time/residue: 1.9879 time to fit residues: 296.0025 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 : 2.097 ------------------------------------------------------------------------------- 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 14 TRP Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain 1 residue 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: 4.9990 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.077727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.058068 restraints weight = 45662.086| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.26 r_work: 0.2753 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 18872 Z= 0.117 Angle : 0.877 44.333 26148 Z= 0.346 Chirality : 0.041 0.399 2517 Planarity : 0.004 0.056 3296 Dihedral : 15.009 174.974 3212 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.84 % Allowed : 14.48 % Favored : 84.68 % 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: 1.80 (0.20), residues: 1897 helix: 2.04 (0.15), residues: 1145 sheet: -0.31 (0.92), residues: 35 loop : -0.06 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 131 HIS 0.004 0.001 HIS A 195 PHE 0.023 0.001 PHE B 246 TYR 0.008 0.001 TYR B 172 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 897) hydrogen bonds : angle 4.27074 ( 2577) covalent geometry : bond 0.00259 (18838) covalent geometry : angle 0.87717 (26148) Misc. bond : bond 0.01977 ( 34) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.873 Fit side-chains REVERT: A 59 ASP cc_start: 0.8626 (p0) cc_final: 0.8409 (p0) REVERT: A 104 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8702 (tm-30) REVERT: C 402 ILE cc_start: 0.2540 (OUTLIER) cc_final: 0.2298 (pp) REVERT: E 8 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7636 (ttt180) REVERT: E 17 ILE cc_start: 0.7942 (mm) cc_final: 0.7725 (tp) REVERT: E 24 SER cc_start: 0.8758 (m) cc_final: 0.8332 (p) REVERT: E 62 GLU cc_start: 0.8666 (mp0) cc_final: 0.8208 (pm20) REVERT: E 77 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8168 (tmtt) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 1.8151 time to fit residues: 258.8179 Evaluate side-chains 122 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 4.814 ------------------------------------------------------------------------------- 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 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 50 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 87 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.076040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.056215 restraints weight = 45806.179| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.30 r_work: 0.2706 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 18872 Z= 0.179 Angle : 0.898 44.514 26148 Z= 0.358 Chirality : 0.043 0.380 2517 Planarity : 0.004 0.057 3296 Dihedral : 15.127 172.426 3212 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.84 % Allowed : 14.29 % Favored : 84.88 % 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: 1.76 (0.19), residues: 1897 helix: 2.00 (0.15), residues: 1136 sheet: -0.32 (0.93), residues: 35 loop : -0.04 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.004 0.001 HIS B 114 PHE 0.024 0.001 PHE B 246 TYR 0.010 0.001 TYR B 172 ARG 0.004 0.000 ARG B 384 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 897) hydrogen bonds : angle 4.37390 ( 2577) covalent geometry : bond 0.00416 (18838) covalent geometry : angle 0.89796 (26148) Misc. bond : bond 0.02635 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13258.59 seconds wall clock time: 239 minutes 40.62 seconds (14380.62 seconds total)