Starting phenix.real_space_refine on Mon Apr 6 11:07:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ua3_63977/04_2026/9ua3_63977.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ua3_63977/04_2026/9ua3_63977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ua3_63977/04_2026/9ua3_63977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ua3_63977/04_2026/9ua3_63977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ua3_63977/04_2026/9ua3_63977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ua3_63977/04_2026/9ua3_63977.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11372 2.51 5 N 3094 2.21 5 O 3338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17924 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4805 Classifications: {'peptide': 616} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 592} Chain: "B" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2574 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 295} Chain breaks: 1 Chain: "E" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4805 Classifications: {'peptide': 616} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 592} Chain: "F" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2574 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 295} Chain breaks: 1 Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 8, 'TRANS': 91} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "G" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 8, 'TRANS': 91} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 3.45, per 1000 atoms: 0.19 Number of scatterers: 17924 At special positions: 0 Unit cell: (193.52, 136.12, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3338 8.00 N 3094 7.00 C 11372 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=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 669.5 milliseconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 8 sheets defined 66.1% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 15 through 26 removed outlier: 3.657A pdb=" N LEU A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 36 removed outlier: 3.712A pdb=" N SER A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.509A pdb=" N ALA A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.505A pdb=" N HIS A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.554A pdb=" N ILE A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.670A pdb=" N MET A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.877A pdb=" N PHE A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 258 removed outlier: 3.913A pdb=" N ASN A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 277 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.906A pdb=" N GLY A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 316 through 330 removed outlier: 3.655A pdb=" N LEU A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.548A pdb=" N ARG A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 372 Processing helix chain 'A' and resid 376 through 400 removed outlier: 4.305A pdb=" N ARG A 397 " --> pdb=" O MET A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 428 removed outlier: 3.742A pdb=" N LEU A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 453 removed outlier: 3.570A pdb=" N GLU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 475 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 484 through 490 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'A' and resid 530 through 538 Processing helix chain 'A' and resid 540 through 550 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 569 through 576 Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'B' and resid 9 through 26 removed outlier: 4.031A pdb=" N THR B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 54 through 78 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.808A pdb=" N GLU B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 155 through 173 removed outlier: 3.506A pdb=" N ILE B 160 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 removed outlier: 3.740A pdb=" N PHE B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 207 through 229 Processing helix chain 'B' and resid 231 through 254 Processing helix chain 'B' and resid 257 through 271 removed outlier: 4.564A pdb=" N LYS B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.622A pdb=" N LEU B 278 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 304 Processing helix chain 'B' and resid 306 through 325 removed outlier: 4.245A pdb=" N HIS B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 325 " --> pdb=" O ASP B 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 Processing helix chain 'E' and resid 15 through 25 Processing helix chain 'E' and resid 27 through 36 Processing helix chain 'E' and resid 43 through 51 removed outlier: 3.658A pdb=" N TYR E 51 " --> pdb=" O MET E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 63 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 118 through 127 Processing helix chain 'E' and resid 128 through 138 Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.851A pdb=" N ILE E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 172 Processing helix chain 'E' and resid 184 through 189 removed outlier: 3.515A pdb=" N ASP E 188 " --> pdb=" O THR E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 removed outlier: 4.214A pdb=" N MET E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 216 through 223 Processing helix chain 'E' and resid 226 through 234 Processing helix chain 'E' and resid 240 through 258 Processing helix chain 'E' and resid 261 through 277 Processing helix chain 'E' and resid 304 through 310 removed outlier: 3.816A pdb=" N LEU E 308 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 316 through 330 removed outlier: 3.595A pdb=" N MET E 320 " --> pdb=" O ASP E 316 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 323 " --> pdb=" O ARG E 319 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 351 removed outlier: 3.842A pdb=" N SER E 338 " --> pdb=" O HIS E 334 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 342 " --> pdb=" O SER E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 372 Processing helix chain 'E' and resid 376 through 400 removed outlier: 4.295A pdb=" N ARG E 397 " --> pdb=" O MET E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 428 removed outlier: 3.641A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 454 removed outlier: 3.773A pdb=" N LYS E 454 " --> pdb=" O CYS E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 474 Processing helix chain 'E' and resid 479 through 483 Processing helix chain 'E' and resid 484 through 490 Processing helix chain 'E' and resid 507 through 518 removed outlier: 3.509A pdb=" N THR E 511 " --> pdb=" O SER E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 538 Processing helix chain 'E' and resid 540 through 551 removed outlier: 3.828A pdb=" N MET E 544 " --> pdb=" O HIS E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 568 Processing helix chain 'E' and resid 569 through 576 removed outlier: 3.926A pdb=" N ASN E 576 " --> pdb=" O GLU E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 606 through 616 Processing helix chain 'F' and resid 9 through 26 removed outlier: 4.363A pdb=" N THR F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 47 Processing helix chain 'F' and resid 53 through 78 removed outlier: 3.507A pdb=" N LEU F 57 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 105 removed outlier: 4.379A pdb=" N LYS F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 Processing helix chain 'F' and resid 138 through 151 Processing helix chain 'F' and resid 155 through 173 removed outlier: 3.740A pdb=" N ARG F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 191 removed outlier: 3.507A pdb=" N ILE F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL F 189 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 207 Processing helix chain 'F' and resid 207 through 229 removed outlier: 3.507A pdb=" N GLU F 229 " --> pdb=" O ASN F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 253 Processing helix chain 'F' and resid 257 through 271 removed outlier: 4.718A pdb=" N LYS F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 288 removed outlier: 3.541A pdb=" N LEU F 278 " --> pdb=" O HIS F 274 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS F 283 " --> pdb=" O HIS F 279 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASN F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 304 removed outlier: 3.958A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 324 removed outlier: 3.711A pdb=" N MET F 311 " --> pdb=" O GLY F 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 36 removed outlier: 4.223A pdb=" N LEU C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 removed outlier: 3.772A pdb=" N GLU C 41 " --> pdb=" O PRO C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.922A pdb=" N GLY C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 66 through 84 Processing helix chain 'D' and resid 99 through 111 Processing helix chain 'G' and resid 23 through 35 removed outlier: 3.766A pdb=" N LEU G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 39 through 46 removed outlier: 3.532A pdb=" N LYS H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 83 removed outlier: 3.897A pdb=" N LEU H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 76 removed outlier: 6.608A pdb=" N VAL A 74 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU A 82 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE A 76 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA3, first strand: chain 'E' and resid 72 through 76 removed outlier: 6.550A pdb=" N VAL E 74 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLU E 82 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE E 76 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR E 80 " --> pdb=" O PHE E 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 18 removed outlier: 4.237A pdb=" N ALA C 73 " --> pdb=" O PHE C 4 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 17 through 18 removed outlier: 6.409A pdb=" N THR C 13 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LYS D 32 " --> pdb=" O THR C 13 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N TYR D 18 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL D 60 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS D 20 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.890A pdb=" N LEU G 5 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR G 16 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR G 13 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS H 20 " --> pdb=" O VAL H 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 80 through 81 988 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5895 1.34 - 1.46: 3591 1.46 - 1.58: 8605 1.58 - 1.70: 1 1.70 - 1.82: 190 Bond restraints: 18282 Sorted by residual: bond pdb=" C LEU F 308 " pdb=" N PRO F 309 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.38e-02 5.25e+03 6.87e+00 bond pdb=" C LEU B 308 " pdb=" N PRO B 309 " ideal model delta sigma weight residual 1.335 1.367 -0.031 1.30e-02 5.92e+03 5.85e+00 bond pdb=" CG1 ILE F 206 " pdb=" CD1 ILE F 206 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.81e+00 bond pdb=" CB ARG G 29 " pdb=" CG ARG G 29 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.64e+00 bond pdb=" CG1 ILE F 42 " pdb=" CD1 ILE F 42 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.26e+00 ... (remaining 18277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 24431 2.87 - 5.74: 243 5.74 - 8.62: 27 8.62 - 11.49: 2 11.49 - 14.36: 1 Bond angle restraints: 24704 Sorted by residual: angle pdb=" CA LEU F 254 " pdb=" CB LEU F 254 " pdb=" CG LEU F 254 " ideal model delta sigma weight residual 116.30 130.66 -14.36 3.50e+00 8.16e-02 1.68e+01 angle pdb=" CB ARG G 29 " pdb=" CG ARG G 29 " pdb=" CD ARG G 29 " ideal model delta sigma weight residual 111.30 119.70 -8.40 2.30e+00 1.89e-01 1.33e+01 angle pdb=" N GLU E 137 " pdb=" CA GLU E 137 " pdb=" CB GLU E 137 " ideal model delta sigma weight residual 110.40 116.33 -5.93 1.63e+00 3.76e-01 1.32e+01 angle pdb=" C ARG A 499 " pdb=" N TYR A 500 " pdb=" CA TYR A 500 " ideal model delta sigma weight residual 122.37 119.05 3.32 9.30e-01 1.16e+00 1.28e+01 angle pdb=" N VAL E 521 " pdb=" CA VAL E 521 " pdb=" C VAL E 521 " ideal model delta sigma weight residual 113.07 108.57 4.50 1.36e+00 5.41e-01 1.09e+01 ... (remaining 24699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9934 17.96 - 35.91: 1026 35.91 - 53.87: 171 53.87 - 71.82: 40 71.82 - 89.78: 13 Dihedral angle restraints: 11184 sinusoidal: 4584 harmonic: 6600 Sorted by residual: dihedral pdb=" CA LEU B 301 " pdb=" C LEU B 301 " pdb=" N ARG B 302 " pdb=" CA ARG B 302 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ALA A 84 " pdb=" C ALA A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ARG G 29 " pdb=" C ARG G 29 " pdb=" N ILE G 30 " pdb=" CA ILE G 30 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 11181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2306 0.055 - 0.111: 411 0.111 - 0.166: 62 0.166 - 0.221: 7 0.221 - 0.277: 2 Chirality restraints: 2788 Sorted by residual: chirality pdb=" CB ILE G 7 " pdb=" CA ILE G 7 " pdb=" CG1 ILE G 7 " pdb=" CG2 ILE G 7 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CG LEU F 254 " pdb=" CB LEU F 254 " pdb=" CD1 LEU F 254 " pdb=" CD2 LEU F 254 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE H 65 " pdb=" CA ILE H 65 " pdb=" CG1 ILE H 65 " pdb=" CG2 ILE H 65 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2785 not shown) Planarity restraints: 3164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 84 " -0.048 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO A 85 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 308 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.73e+00 pdb=" N PRO F 309 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 309 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 309 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 476 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO E 477 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 477 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 477 " 0.035 5.00e-02 4.00e+02 ... (remaining 3161 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 994 2.73 - 3.27: 18583 3.27 - 3.82: 30967 3.82 - 4.36: 36777 4.36 - 4.90: 62195 Nonbonded interactions: 149516 Sorted by model distance: nonbonded pdb=" OG1 THR A 227 " pdb=" OH TYR A 268 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR A 277 " pdb=" OD1 ASN A 303 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR E 227 " pdb=" OH TYR E 268 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR B 219 " pdb=" OE1 GLU B 246 " model vdw 2.224 3.040 nonbonded pdb=" O HIS A 148 " pdb=" OG SER A 179 " model vdw 2.243 3.040 ... (remaining 149511 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.070 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.004 0.065 18282 Z= 0.179 Angle : 0.729 14.360 24704 Z= 0.392 Chirality : 0.044 0.277 2788 Planarity : 0.006 0.073 3164 Dihedral : 14.783 89.779 6900 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2220 helix: -0.46 (0.13), residues: 1401 sheet: -2.67 (0.68), residues: 50 loop : -0.90 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 269 TYR 0.024 0.001 TYR A 296 PHE 0.026 0.002 PHE E 386 TRP 0.027 0.002 TRP F 35 HIS 0.006 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00402 (18282) covalent geometry : angle 0.72884 (24704) hydrogen bonds : bond 0.17892 ( 986) hydrogen bonds : angle 6.87957 ( 2913) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: B 236 MET cc_start: 0.6475 (ttt) cc_final: 0.6274 (ttt) REVERT: C 31 VAL cc_start: 0.7792 (t) cc_final: 0.7531 (m) REVERT: D 67 SER cc_start: 0.8113 (m) cc_final: 0.7839 (m) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1235 time to fit residues: 62.2298 Evaluate side-chains 259 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 264 HIS ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 313 GLN E 579 GLN F 234 GLN D 68 HIS ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.178694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135102 restraints weight = 23685.103| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.11 r_work: 0.3315 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18282 Z= 0.146 Angle : 0.555 6.663 24704 Z= 0.293 Chirality : 0.039 0.155 2788 Planarity : 0.005 0.060 3164 Dihedral : 4.471 28.457 2434 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.56 % Allowed : 7.98 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2220 helix: 0.23 (0.13), residues: 1462 sheet: -1.92 (0.77), residues: 40 loop : -0.92 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.025 0.001 TYR F 219 PHE 0.024 0.001 PHE E 76 TRP 0.018 0.002 TRP A 88 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00330 (18282) covalent geometry : angle 0.55478 (24704) hydrogen bonds : bond 0.04514 ( 986) hydrogen bonds : angle 4.76466 ( 2913) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 277 time to evaluate : 0.616 Fit side-chains REVERT: A 111 ASN cc_start: 0.7740 (t0) cc_final: 0.6936 (p0) REVERT: A 126 ASP cc_start: 0.8138 (m-30) cc_final: 0.7646 (m-30) REVERT: A 426 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8249 (mp) REVERT: B 26 MET cc_start: 0.8874 (mpp) cc_final: 0.8637 (mpp) REVERT: B 228 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7612 (pp30) REVERT: E 303 ASN cc_start: 0.8040 (t0) cc_final: 0.7692 (t0) REVERT: C 31 VAL cc_start: 0.7546 (t) cc_final: 0.7151 (p) REVERT: D 67 SER cc_start: 0.8104 (m) cc_final: 0.7880 (m) outliers start: 11 outliers final: 7 residues processed: 282 average time/residue: 0.1215 time to fit residues: 53.2794 Evaluate side-chains 259 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 250 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain D residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 134 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 158 optimal weight: 0.5980 chunk 211 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 chunk 199 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS E 236 HIS ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.178106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134199 restraints weight = 23707.627| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.72 r_work: 0.3359 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18282 Z= 0.145 Angle : 0.523 7.468 24704 Z= 0.274 Chirality : 0.039 0.142 2788 Planarity : 0.004 0.057 3164 Dihedral : 4.332 30.723 2434 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.06 % Allowed : 10.05 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2220 helix: 0.64 (0.14), residues: 1460 sheet: -1.80 (0.80), residues: 40 loop : -0.83 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 161 TYR 0.024 0.001 TYR B 219 PHE 0.023 0.001 PHE F 10 TRP 0.020 0.002 TRP A 88 HIS 0.006 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00338 (18282) covalent geometry : angle 0.52289 (24704) hydrogen bonds : bond 0.03949 ( 986) hydrogen bonds : angle 4.44057 ( 2913) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 0.706 Fit side-chains REVERT: A 111 ASN cc_start: 0.7722 (t0) cc_final: 0.6931 (p0) REVERT: A 126 ASP cc_start: 0.8151 (m-30) cc_final: 0.7797 (m-30) REVERT: A 297 ASP cc_start: 0.8480 (t0) cc_final: 0.8272 (t0) REVERT: B 26 MET cc_start: 0.8714 (mpp) cc_final: 0.8355 (mpp) REVERT: E 99 VAL cc_start: 0.8573 (t) cc_final: 0.8357 (p) REVERT: E 104 ASN cc_start: 0.9171 (m110) cc_final: 0.8931 (m110) REVERT: E 303 ASN cc_start: 0.7998 (t0) cc_final: 0.7643 (t0) REVERT: C 31 VAL cc_start: 0.7557 (t) cc_final: 0.7175 (p) REVERT: D 67 SER cc_start: 0.8100 (m) cc_final: 0.7866 (m) REVERT: D 95 ILE cc_start: 0.8769 (mm) cc_final: 0.8550 (mm) outliers start: 21 outliers final: 14 residues processed: 277 average time/residue: 0.1274 time to fit residues: 55.0286 Evaluate side-chains 264 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 616 HIS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 67 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 140 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS C 49 GLN D 108 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.178844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133193 restraints weight = 23632.819| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.81 r_work: 0.3361 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18282 Z= 0.122 Angle : 0.502 7.141 24704 Z= 0.261 Chirality : 0.038 0.146 2788 Planarity : 0.004 0.057 3164 Dihedral : 4.236 31.366 2434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.36 % Allowed : 11.16 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2220 helix: 0.89 (0.14), residues: 1458 sheet: -1.70 (0.82), residues: 40 loop : -0.76 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 89 TYR 0.022 0.001 TYR B 219 PHE 0.015 0.001 PHE F 10 TRP 0.021 0.001 TRP A 88 HIS 0.006 0.001 HIS E 540 Details of bonding type rmsd covalent geometry : bond 0.00283 (18282) covalent geometry : angle 0.50232 (24704) hydrogen bonds : bond 0.03683 ( 986) hydrogen bonds : angle 4.25459 ( 2913) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 0.708 Fit side-chains REVERT: A 47 MET cc_start: 0.6909 (mmm) cc_final: 0.6707 (mmm) REVERT: A 111 ASN cc_start: 0.7714 (t0) cc_final: 0.6902 (p0) REVERT: A 126 ASP cc_start: 0.8257 (m-30) cc_final: 0.8035 (m-30) REVERT: A 297 ASP cc_start: 0.8526 (t0) cc_final: 0.8306 (t0) REVERT: A 587 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.6483 (mp-120) REVERT: B 294 MET cc_start: 0.7586 (mtm) cc_final: 0.7378 (mtt) REVERT: E 99 VAL cc_start: 0.8607 (t) cc_final: 0.8385 (p) REVERT: E 104 ASN cc_start: 0.9189 (m110) cc_final: 0.8949 (m110) REVERT: E 303 ASN cc_start: 0.7981 (t0) cc_final: 0.7607 (t0) REVERT: F 4 LYS cc_start: 0.8495 (tptt) cc_final: 0.8149 (tppt) REVERT: F 234 GLN cc_start: 0.8790 (mp10) cc_final: 0.8399 (mm-40) REVERT: C 31 VAL cc_start: 0.7411 (t) cc_final: 0.7039 (p) REVERT: D 67 SER cc_start: 0.8102 (m) cc_final: 0.7876 (m) REVERT: D 95 ILE cc_start: 0.8777 (mm) cc_final: 0.8539 (mm) REVERT: D 108 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7261 (m-40) REVERT: H 22 ILE cc_start: 0.8308 (mp) cc_final: 0.7938 (mp) REVERT: H 59 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7225 (tm-30) outliers start: 27 outliers final: 16 residues processed: 287 average time/residue: 0.1274 time to fit residues: 56.8240 Evaluate side-chains 270 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 616 HIS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain H residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 98 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 27 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS C 49 GLN D 108 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.178499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136377 restraints weight = 23516.169| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.82 r_work: 0.3344 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18282 Z= 0.132 Angle : 0.505 6.815 24704 Z= 0.263 Chirality : 0.038 0.140 2788 Planarity : 0.004 0.058 3164 Dihedral : 4.169 32.102 2434 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.92 % Allowed : 11.62 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2220 helix: 0.99 (0.14), residues: 1460 sheet: -1.66 (0.82), residues: 40 loop : -0.70 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 177 TYR 0.019 0.001 TYR B 219 PHE 0.014 0.001 PHE F 202 TRP 0.021 0.001 TRP A 88 HIS 0.006 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00310 (18282) covalent geometry : angle 0.50533 (24704) hydrogen bonds : bond 0.03627 ( 986) hydrogen bonds : angle 4.19019 ( 2913) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7713 (t0) cc_final: 0.6993 (p0) REVERT: A 297 ASP cc_start: 0.8578 (t0) cc_final: 0.8376 (t0) REVERT: B 322 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: E 99 VAL cc_start: 0.8675 (t) cc_final: 0.8447 (p) REVERT: E 104 ASN cc_start: 0.9131 (m110) cc_final: 0.8919 (m110) REVERT: E 303 ASN cc_start: 0.8018 (t0) cc_final: 0.7651 (t0) REVERT: E 610 GLU cc_start: 0.8190 (pp20) cc_final: 0.7946 (pp20) REVERT: F 4 LYS cc_start: 0.8515 (tptt) cc_final: 0.8177 (tppt) REVERT: F 26 MET cc_start: 0.8849 (mtm) cc_final: 0.8504 (mpp) REVERT: F 234 GLN cc_start: 0.8697 (mp10) cc_final: 0.8341 (mm-40) REVERT: C 31 VAL cc_start: 0.7491 (t) cc_final: 0.7091 (p) REVERT: C 49 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7309 (pp30) REVERT: D 67 SER cc_start: 0.8199 (m) cc_final: 0.7961 (m) REVERT: H 22 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8193 (mp) outliers start: 38 outliers final: 21 residues processed: 281 average time/residue: 0.1212 time to fit residues: 53.2282 Evaluate side-chains 276 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 616 HIS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 93 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS C 49 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.177669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132811 restraints weight = 23557.223| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.85 r_work: 0.3340 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18282 Z= 0.143 Angle : 0.515 6.834 24704 Z= 0.266 Chirality : 0.038 0.151 2788 Planarity : 0.004 0.057 3164 Dihedral : 4.162 33.137 2434 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.87 % Allowed : 12.78 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2220 helix: 1.06 (0.14), residues: 1460 sheet: -1.62 (0.81), residues: 40 loop : -0.68 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 269 TYR 0.019 0.001 TYR F 219 PHE 0.013 0.001 PHE F 64 TRP 0.022 0.002 TRP A 88 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00340 (18282) covalent geometry : angle 0.51488 (24704) hydrogen bonds : bond 0.03613 ( 986) hydrogen bonds : angle 4.15928 ( 2913) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 57 VAL cc_start: 0.6631 (OUTLIER) cc_final: 0.6266 (p) REVERT: A 111 ASN cc_start: 0.7689 (t0) cc_final: 0.6942 (p0) REVERT: A 124 CYS cc_start: 0.8446 (m) cc_final: 0.7923 (m) REVERT: A 137 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8343 (mm-30) REVERT: A 297 ASP cc_start: 0.8616 (t0) cc_final: 0.8385 (t0) REVERT: B 294 MET cc_start: 0.7561 (mtm) cc_final: 0.7273 (mtt) REVERT: B 322 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: E 99 VAL cc_start: 0.8679 (t) cc_final: 0.8455 (p) REVERT: E 303 ASN cc_start: 0.8044 (t0) cc_final: 0.7682 (t0) REVERT: E 610 GLU cc_start: 0.8241 (pp20) cc_final: 0.7969 (pp20) REVERT: F 4 LYS cc_start: 0.8532 (tptt) cc_final: 0.8232 (tptm) REVERT: F 234 GLN cc_start: 0.8784 (mp10) cc_final: 0.8445 (mm110) REVERT: C 31 VAL cc_start: 0.7398 (t) cc_final: 0.6998 (p) REVERT: D 67 SER cc_start: 0.8149 (m) cc_final: 0.7923 (m) REVERT: H 22 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8058 (mp) REVERT: H 59 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7572 (tm-30) outliers start: 37 outliers final: 23 residues processed: 284 average time/residue: 0.1266 time to fit residues: 56.2050 Evaluate side-chains 281 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 616 HIS Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 22 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** A 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS C 49 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131523 restraints weight = 23717.469| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.69 r_work: 0.3351 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18282 Z= 0.153 Angle : 0.528 7.431 24704 Z= 0.272 Chirality : 0.039 0.145 2788 Planarity : 0.004 0.054 3164 Dihedral : 4.157 34.531 2434 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.97 % Allowed : 13.33 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2220 helix: 1.10 (0.14), residues: 1464 sheet: -1.88 (0.83), residues: 38 loop : -0.65 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 269 TYR 0.021 0.001 TYR B 219 PHE 0.013 0.001 PHE F 64 TRP 0.029 0.002 TRP A 88 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00368 (18282) covalent geometry : angle 0.52843 (24704) hydrogen bonds : bond 0.03616 ( 986) hydrogen bonds : angle 4.14558 ( 2913) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 0.667 Fit side-chains REVERT: A 51 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: A 57 VAL cc_start: 0.6689 (OUTLIER) cc_final: 0.6335 (p) REVERT: A 111 ASN cc_start: 0.7678 (t0) cc_final: 0.6929 (p0) REVERT: A 124 CYS cc_start: 0.8463 (m) cc_final: 0.7913 (m) REVERT: A 137 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8260 (mm-30) REVERT: A 297 ASP cc_start: 0.8602 (t0) cc_final: 0.8360 (t0) REVERT: A 587 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.6811 (mp10) REVERT: B 294 MET cc_start: 0.7625 (mtm) cc_final: 0.7337 (mtt) REVERT: B 322 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7537 (mt-10) REVERT: E 99 VAL cc_start: 0.8669 (t) cc_final: 0.8446 (p) REVERT: E 303 ASN cc_start: 0.8058 (t0) cc_final: 0.7703 (t0) REVERT: E 610 GLU cc_start: 0.8296 (pp20) cc_final: 0.7999 (pp20) REVERT: F 4 LYS cc_start: 0.8497 (tptt) cc_final: 0.8160 (tppt) REVERT: F 234 GLN cc_start: 0.8841 (mp10) cc_final: 0.8481 (mm110) REVERT: C 31 VAL cc_start: 0.7433 (t) cc_final: 0.7064 (p) REVERT: D 67 SER cc_start: 0.8184 (m) cc_final: 0.7932 (m) REVERT: H 22 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8091 (mp) outliers start: 39 outliers final: 23 residues processed: 295 average time/residue: 0.1243 time to fit residues: 57.2611 Evaluate side-chains 290 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 616 HIS Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** B 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN C 49 GLN D 85 ASN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.176407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130844 restraints weight = 23700.571| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.66 r_work: 0.3348 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18282 Z= 0.162 Angle : 0.537 7.084 24704 Z= 0.277 Chirality : 0.039 0.167 2788 Planarity : 0.004 0.054 3164 Dihedral : 4.174 35.049 2434 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.77 % Allowed : 14.19 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2220 helix: 1.14 (0.14), residues: 1462 sheet: -1.70 (0.80), residues: 40 loop : -0.63 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 89 TYR 0.020 0.001 TYR B 219 PHE 0.015 0.001 PHE F 202 TRP 0.031 0.002 TRP A 88 HIS 0.006 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00391 (18282) covalent geometry : angle 0.53724 (24704) hydrogen bonds : bond 0.03657 ( 986) hydrogen bonds : angle 4.14572 ( 2913) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 57 VAL cc_start: 0.6583 (OUTLIER) cc_final: 0.6216 (p) REVERT: A 111 ASN cc_start: 0.7655 (t0) cc_final: 0.6940 (p0) REVERT: A 124 CYS cc_start: 0.8395 (m) cc_final: 0.7842 (m) REVERT: A 137 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8272 (mm-30) REVERT: A 587 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.6791 (mp10) REVERT: B 294 MET cc_start: 0.7581 (mtm) cc_final: 0.7288 (mtt) REVERT: B 322 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: E 104 ASN cc_start: 0.9117 (m110) cc_final: 0.8902 (m110) REVERT: E 303 ASN cc_start: 0.8004 (t0) cc_final: 0.7638 (t0) REVERT: E 562 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: E 610 GLU cc_start: 0.8281 (pp20) cc_final: 0.7978 (pp20) REVERT: F 4 LYS cc_start: 0.8536 (tptt) cc_final: 0.8181 (tppt) REVERT: F 234 GLN cc_start: 0.8795 (mp10) cc_final: 0.8446 (mm110) REVERT: C 31 VAL cc_start: 0.7467 (t) cc_final: 0.7085 (p) REVERT: D 67 SER cc_start: 0.8189 (m) cc_final: 0.7932 (m) REVERT: D 108 ASN cc_start: 0.8177 (m-40) cc_final: 0.7873 (m-40) REVERT: H 22 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8101 (mp) REVERT: H 59 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7473 (tm-30) REVERT: H 108 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8547 (t0) outliers start: 35 outliers final: 21 residues processed: 285 average time/residue: 0.1301 time to fit residues: 57.0555 Evaluate side-chains 289 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 262 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 562 GLN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 108 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 155 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 chunk 198 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN C 49 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.177285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132458 restraints weight = 23630.137| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.68 r_work: 0.3355 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18282 Z= 0.136 Angle : 0.545 17.102 24704 Z= 0.278 Chirality : 0.039 0.159 2788 Planarity : 0.004 0.052 3164 Dihedral : 4.155 29.682 2434 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.57 % Allowed : 14.65 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 2220 helix: 1.18 (0.14), residues: 1458 sheet: -1.68 (0.79), residues: 40 loop : -0.59 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 89 TYR 0.019 0.001 TYR B 219 PHE 0.014 0.001 PHE F 202 TRP 0.034 0.002 TRP A 88 HIS 0.006 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00323 (18282) covalent geometry : angle 0.54525 (24704) hydrogen bonds : bond 0.03635 ( 986) hydrogen bonds : angle 4.12590 ( 2913) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 57 VAL cc_start: 0.6587 (OUTLIER) cc_final: 0.6230 (p) REVERT: A 111 ASN cc_start: 0.7681 (t0) cc_final: 0.6996 (p0) REVERT: A 124 CYS cc_start: 0.8420 (m) cc_final: 0.7919 (m) REVERT: A 137 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8283 (mm-30) REVERT: A 587 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6811 (mp10) REVERT: B 294 MET cc_start: 0.7610 (mtm) cc_final: 0.7320 (mtt) REVERT: E 303 ASN cc_start: 0.7991 (t0) cc_final: 0.7623 (t0) REVERT: E 562 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: E 610 GLU cc_start: 0.8300 (pp20) cc_final: 0.7973 (pp20) REVERT: F 234 GLN cc_start: 0.8825 (mp10) cc_final: 0.8465 (mm110) REVERT: C 31 VAL cc_start: 0.7437 (t) cc_final: 0.7061 (p) REVERT: D 67 SER cc_start: 0.8198 (m) cc_final: 0.7941 (m) REVERT: H 22 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8041 (mp) REVERT: H 92 GLU cc_start: 0.8327 (tt0) cc_final: 0.7848 (pp20) outliers start: 31 outliers final: 22 residues processed: 277 average time/residue: 0.1327 time to fit residues: 56.3462 Evaluate side-chains 282 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 562 GLN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 154 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 214 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN C 49 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132082 restraints weight = 23483.296| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.63 r_work: 0.3359 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 18282 Z= 0.182 Angle : 0.785 59.200 24704 Z= 0.450 Chirality : 0.040 0.374 2788 Planarity : 0.005 0.156 3164 Dihedral : 4.155 28.954 2434 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.57 % Allowed : 14.65 % Favored : 83.79 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2220 helix: 1.19 (0.14), residues: 1458 sheet: -1.67 (0.79), residues: 40 loop : -0.59 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 89 TYR 0.018 0.001 TYR B 219 PHE 0.016 0.001 PHE F 202 TRP 0.031 0.002 TRP A 88 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00427 (18282) covalent geometry : angle 0.78510 (24704) hydrogen bonds : bond 0.03636 ( 986) hydrogen bonds : angle 4.12659 ( 2913) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 57 VAL cc_start: 0.6578 (OUTLIER) cc_final: 0.6216 (p) REVERT: A 111 ASN cc_start: 0.7686 (t0) cc_final: 0.7009 (p0) REVERT: A 124 CYS cc_start: 0.8430 (m) cc_final: 0.7934 (m) REVERT: A 137 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8286 (mm-30) REVERT: A 587 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6819 (mp10) REVERT: B 294 MET cc_start: 0.7595 (mtm) cc_final: 0.7305 (mtt) REVERT: B 322 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: E 303 ASN cc_start: 0.7981 (t0) cc_final: 0.7611 (t0) REVERT: E 562 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: E 610 GLU cc_start: 0.8276 (pp20) cc_final: 0.7945 (pp20) REVERT: F 234 GLN cc_start: 0.8783 (mp10) cc_final: 0.8438 (mm110) REVERT: C 31 VAL cc_start: 0.7452 (t) cc_final: 0.7074 (p) REVERT: D 67 SER cc_start: 0.8181 (m) cc_final: 0.7924 (m) REVERT: H 22 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8059 (mp) REVERT: H 92 GLU cc_start: 0.8359 (tt0) cc_final: 0.7853 (pp20) outliers start: 31 outliers final: 24 residues processed: 271 average time/residue: 0.1275 time to fit residues: 52.9119 Evaluate side-chains 282 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 376 SER Chi-restraints excluded: chain E residue 503 CYS Chi-restraints excluded: chain E residue 562 GLN Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain C residue 6 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.648 > 50: distance: 101 - 122: 19.336 distance: 109 - 131: 26.799 distance: 116 - 122: 20.166 distance: 122 - 123: 7.299 distance: 123 - 124: 22.293 distance: 123 - 126: 11.988 distance: 124 - 125: 18.715 distance: 124 - 131: 35.199 distance: 125 - 152: 26.546 distance: 126 - 127: 43.251 distance: 127 - 128: 25.161 distance: 128 - 129: 4.864 distance: 128 - 130: 13.145 distance: 131 - 132: 28.481 distance: 132 - 133: 10.670 distance: 133 - 134: 49.772 distance: 133 - 136: 46.081 distance: 136 - 137: 17.677 distance: 137 - 138: 15.584 distance: 137 - 140: 31.264 distance: 138 - 144: 24.137 distance: 139 - 171: 29.313 distance: 140 - 141: 15.222 distance: 141 - 142: 43.413 distance: 141 - 143: 62.731 distance: 144 - 145: 24.078 distance: 145 - 146: 23.917 distance: 145 - 148: 8.873 distance: 146 - 147: 13.242 distance: 146 - 152: 24.377 distance: 147 - 180: 50.979 distance: 148 - 149: 34.816 distance: 149 - 150: 30.091 distance: 149 - 151: 29.753 distance: 152 - 153: 15.638 distance: 153 - 154: 15.561 distance: 153 - 156: 15.734 distance: 154 - 155: 10.434 distance: 154 - 160: 14.552 distance: 155 - 191: 26.760 distance: 156 - 157: 25.299 distance: 156 - 158: 31.029 distance: 157 - 159: 38.212 distance: 160 - 161: 20.177 distance: 161 - 162: 27.305 distance: 161 - 164: 16.242 distance: 162 - 163: 14.480 distance: 162 - 171: 12.212 distance: 163 - 199: 49.947 distance: 164 - 165: 34.386 distance: 165 - 166: 17.745 distance: 166 - 167: 32.861 distance: 167 - 168: 15.488 distance: 168 - 169: 28.763 distance: 168 - 170: 30.629 distance: 171 - 172: 24.096 distance: 172 - 173: 35.224 distance: 172 - 175: 16.602 distance: 173 - 174: 14.779 distance: 173 - 180: 4.339 distance: 175 - 176: 30.796 distance: 176 - 177: 38.390 distance: 177 - 178: 14.328 distance: 177 - 179: 20.942 distance: 180 - 181: 10.902 distance: 181 - 182: 30.944 distance: 181 - 184: 32.371 distance: 182 - 183: 31.423 distance: 182 - 191: 28.268 distance: 184 - 185: 8.377 distance: 185 - 186: 7.396 distance: 186 - 187: 39.627 distance: 187 - 188: 12.965 distance: 188 - 189: 3.604 distance: 188 - 190: 17.630 distance: 191 - 192: 22.534 distance: 192 - 193: 51.770 distance: 192 - 195: 4.984 distance: 193 - 194: 28.407 distance: 193 - 199: 20.662 distance: 195 - 196: 24.368 distance: 195 - 197: 36.571 distance: 196 - 198: 31.928 distance: 199 - 200: 41.004 distance: 200 - 201: 46.832 distance: 200 - 203: 42.896 distance: 201 - 202: 47.908 distance: 201 - 207: 23.611 distance: 203 - 204: 4.449 distance: 204 - 205: 52.378 distance: 204 - 206: 43.527