Starting phenix.real_space_refine on Tue Nov 18 18:48:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey2_50052/11_2025/9ey2_50052.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey2_50052/11_2025/9ey2_50052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ey2_50052/11_2025/9ey2_50052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey2_50052/11_2025/9ey2_50052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ey2_50052/11_2025/9ey2_50052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey2_50052/11_2025/9ey2_50052.map" } resolution = 2.96 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= 0.012 sd= 0.338 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 71 5.49 5 S 85 5.16 5 C 10210 2.51 5 N 2906 2.21 5 O 3281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16555 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "F" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2355 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Chain breaks: 1 Chain: "T" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1437 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 27} Link IDs: {'rna2p': 17, 'rna3p': 50} Chain breaks: 1 Chain: "E" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5310 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.61, per 1000 atoms: 0.28 Number of scatterers: 16555 At special positions: 0 Unit cell: (104.34, 119.045, 170.865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 85 16.00 P 71 15.00 O 3281 8.00 N 2906 7.00 C 10210 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 887.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" ND1 HIS E 724 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 551 " pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 644 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 546 " pdb="ZN ZN E 902 " - pdb=" ND1 HIS E 548 " 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 14 sheets defined 49.6% alpha, 14.1% beta 17 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.718A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 138 removed outlier: 3.550A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.662A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.678A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.659A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 138 removed outlier: 3.560A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.615A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.663A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 138 removed outlier: 3.547A pdb=" N GLY C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 125 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.641A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.655A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.722A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.723A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 138 removed outlier: 3.543A pdb=" N GLY D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 187 removed outlier: 4.626A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.658A pdb=" N TYR D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 4.035A pdb=" N GLU F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.608A pdb=" N THR F 119 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS F 123 " --> pdb=" O THR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 164 removed outlier: 3.527A pdb=" N GLU F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 202 Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 216 through 236 removed outlier: 3.563A pdb=" N ASN F 222 " --> pdb=" O LYS F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 removed outlier: 4.083A pdb=" N LYS F 268 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 282 removed outlier: 3.524A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 374 through 376 No H-bonds generated for 'chain 'F' and resid 374 through 376' Processing helix chain 'F' and resid 377 through 379 No H-bonds generated for 'chain 'F' and resid 377 through 379' Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.847A pdb=" N LEU E 126 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 127 " --> pdb=" O GLY E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.980A pdb=" N ILE E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 271 through 281 removed outlier: 3.506A pdb=" N ALA E 277 " --> pdb=" O PRO E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 289 removed outlier: 3.652A pdb=" N GLY E 288 " --> pdb=" O THR E 285 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 289 " --> pdb=" O HIS E 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 285 through 289' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.944A pdb=" N TYR E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 351 removed outlier: 3.747A pdb=" N ASP E 351 " --> pdb=" O SER E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 361 removed outlier: 3.815A pdb=" N PHE E 361 " --> pdb=" O TRP E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 393 removed outlier: 3.686A pdb=" N LEU E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE E 392 " --> pdb=" O GLN E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 Processing helix chain 'E' and resid 455 through 468 Processing helix chain 'E' and resid 519 through 529 Processing helix chain 'E' and resid 531 through 538 Processing helix chain 'E' and resid 554 through 570 Processing helix chain 'E' and resid 582 through 595 removed outlier: 3.741A pdb=" N ALA E 586 " --> pdb=" O ASN E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 600 No H-bonds generated for 'chain 'E' and resid 598 through 600' Processing helix chain 'E' and resid 608 through 611 removed outlier: 3.599A pdb=" N GLN E 611 " --> pdb=" O LYS E 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 608 through 611' Processing helix chain 'E' and resid 618 through 633 Processing helix chain 'E' and resid 670 through 677 Processing helix chain 'E' and resid 693 through 701 removed outlier: 3.939A pdb=" N GLU E 699 " --> pdb=" O GLU E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 715 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 759 through 762 Processing helix chain 'E' and resid 763 through 771 Processing helix chain 'E' and resid 771 through 791 removed outlier: 3.641A pdb=" N GLU E 777 " --> pdb=" O GLY E 773 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.671A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.668A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.687A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.686A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'F' and resid 272 through 273 removed outlier: 8.713A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 342 through 344 removed outlier: 5.086A pdb=" N GLY F 383 " --> pdb=" O GLN F 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 162 through 167 removed outlier: 3.590A pdb=" N GLY E 140 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP E 106 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N SER E 139 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE E 108 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ARG E 82 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE E 108 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU E 84 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA E 73 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 58 " --> pdb=" O LEU E 427 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.608A pdb=" N TYR E 173 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA E 305 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N VAL E 341 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL E 307 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS E 367 " --> pdb=" O VAL E 417 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 602 through 606 removed outlier: 6.019A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA E 540 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL E 579 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL E 542 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER E 511 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N PHE E 543 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU E 513 " --> pdb=" O PHE E 543 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR E 510 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET E 750 " --> pdb=" O PHE E 485 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 634 through 641 removed outlier: 6.822A pdb=" N VAL E 654 " --> pdb=" O GLU E 635 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 637 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA E 652 " --> pdb=" O PHE E 637 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR E 639 " --> pdb=" O GLY E 650 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY E 650 " --> pdb=" O THR E 639 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LYS E 660 " --> pdb=" O LEU E 682 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE E 684 " --> pdb=" O LYS E 660 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL E 662 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N GLU E 686 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU E 683 " --> pdb=" O MET E 721 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASN E 723 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS E 685 " --> pdb=" O ASN E 723 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE E 720 " --> pdb=" O GLY E 744 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 2154 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3266 1.33 - 1.45: 4502 1.45 - 1.57: 8948 1.57 - 1.70: 141 1.70 - 1.82: 136 Bond restraints: 16993 Sorted by residual: bond pdb=" CG HIS E 551 " pdb=" CD2 HIS E 551 " ideal model delta sigma weight residual 1.354 1.296 0.058 1.10e-02 8.26e+03 2.78e+01 bond pdb=" CB HIS E 551 " pdb=" CG HIS E 551 " ideal model delta sigma weight residual 1.497 1.429 0.068 1.40e-02 5.10e+03 2.37e+01 bond pdb=" CG HIS E 724 " pdb=" ND1 HIS E 724 " ideal model delta sigma weight residual 1.378 1.425 -0.047 1.10e-02 8.26e+03 1.80e+01 bond pdb=" CD2 HIS E 551 " pdb=" NE2 HIS E 551 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.10e-02 8.26e+03 1.55e+01 bond pdb=" N GLY E 489 " pdb=" CA GLY E 489 " ideal model delta sigma weight residual 1.444 1.479 -0.035 1.02e-02 9.61e+03 1.20e+01 ... (remaining 16988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 22592 2.63 - 5.26: 722 5.26 - 7.89: 16 7.89 - 10.52: 9 10.52 - 13.15: 2 Bond angle restraints: 23341 Sorted by residual: angle pdb=" N SER E 500 " pdb=" CA SER E 500 " pdb=" C SER E 500 " ideal model delta sigma weight residual 109.25 118.32 -9.07 1.53e+00 4.27e-01 3.51e+01 angle pdb=" N HIS E 527 " pdb=" CA HIS E 527 " pdb=" C HIS E 527 " ideal model delta sigma weight residual 111.69 105.32 6.37 1.23e+00 6.61e-01 2.68e+01 angle pdb=" CA ALA E 491 " pdb=" C ALA E 491 " pdb=" N ILE E 492 " ideal model delta sigma weight residual 119.98 116.10 3.88 8.50e-01 1.38e+00 2.08e+01 angle pdb=" PA GTP T 101 " pdb=" O3A GTP T 101 " pdb=" PB GTP T 101 " ideal model delta sigma weight residual 120.50 133.65 -13.15 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CB HIS E 724 " pdb=" CG HIS E 724 " pdb=" ND1 HIS E 724 " ideal model delta sigma weight residual 122.70 129.18 -6.48 1.50e+00 4.44e-01 1.87e+01 ... (remaining 23336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 10021 35.45 - 70.91: 284 70.91 - 106.36: 33 106.36 - 141.82: 5 141.82 - 177.27: 3 Dihedral angle restraints: 10346 sinusoidal: 4723 harmonic: 5623 Sorted by residual: dihedral pdb=" O4' C T 44 " pdb=" C1' C T 44 " pdb=" N1 C T 44 " pdb=" C2 C T 44 " ideal model delta sinusoidal sigma weight residual 232.00 54.73 177.27 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C T 69 " pdb=" C1' C T 69 " pdb=" N1 C T 69 " pdb=" C2 C T 69 " ideal model delta sinusoidal sigma weight residual -128.00 36.28 -164.28 1 1.70e+01 3.46e-03 6.52e+01 dihedral pdb=" O4' C T 71 " pdb=" C1' C T 71 " pdb=" N1 C T 71 " pdb=" C2 C T 71 " ideal model delta sinusoidal sigma weight residual -128.00 27.72 -155.72 1 1.70e+01 3.46e-03 6.35e+01 ... (remaining 10343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2628 0.117 - 0.235: 107 0.235 - 0.352: 0 0.352 - 0.469: 1 0.469 - 0.586: 1 Chirality restraints: 2737 Sorted by residual: chirality pdb=" P A T 19 " pdb=" OP1 A T 19 " pdb=" OP2 A T 19 " pdb=" O5' A T 19 " both_signs ideal model delta sigma weight residual True 2.41 3.00 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" P U T 2 " pdb=" OP1 U T 2 " pdb=" OP2 U T 2 " pdb=" O5' U T 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CA SAM F 501 " pdb=" N SAM F 501 " pdb=" C SAM F 501 " pdb=" CB SAM F 501 " both_signs ideal model delta sigma weight residual False 2.45 2.66 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2734 not shown) Planarity restraints: 2783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A T 28 " -0.069 2.00e-02 2.50e+03 3.08e-02 2.61e+01 pdb=" N9 A T 28 " 0.070 2.00e-02 2.50e+03 pdb=" C8 A T 28 " 0.010 2.00e-02 2.50e+03 pdb=" N7 A T 28 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A T 28 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A T 28 " -0.017 2.00e-02 2.50e+03 pdb=" N6 A T 28 " -0.015 2.00e-02 2.50e+03 pdb=" N1 A T 28 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A T 28 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A T 28 " 0.009 2.00e-02 2.50e+03 pdb=" C4 A T 28 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 659 " -0.053 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP E 659 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP E 659 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP E 659 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP E 659 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 659 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 659 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 659 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 659 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 659 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 128 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C LEU E 128 " 0.074 2.00e-02 2.50e+03 pdb=" O LEU E 128 " -0.028 2.00e-02 2.50e+03 pdb=" N LYS E 129 " -0.025 2.00e-02 2.50e+03 ... (remaining 2780 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 372 2.65 - 3.21: 14988 3.21 - 3.78: 27242 3.78 - 4.34: 39523 4.34 - 4.90: 61244 Nonbonded interactions: 143369 Sorted by model distance: nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 901 " model vdw 2.088 2.230 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 902 " model vdw 2.113 2.230 nonbonded pdb=" OG1 THR D 153 " pdb=" OH TYR D 233 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR C 153 " pdb=" OH TYR C 233 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR B 153 " pdb=" OH TYR B 233 " model vdw 2.207 3.040 ... (remaining 143364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 19.610 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.580 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.011 0.593 16999 Z= 0.612 Angle : 1.166 13.146 23341 Z= 0.827 Chirality : 0.060 0.586 2737 Planarity : 0.011 0.119 2783 Dihedral : 16.732 177.273 6732 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.17), residues: 1962 helix: -0.34 (0.15), residues: 869 sheet: 0.66 (0.30), residues: 303 loop : -1.05 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG B 29 TYR 0.051 0.006 TYR E 59 PHE 0.057 0.008 PHE B 159 TRP 0.059 0.008 TRP E 659 HIS 0.051 0.006 HIS E 724 Details of bonding type rmsd covalent geometry : bond 0.00910 (16993) covalent geometry : angle 1.16600 (23341) hydrogen bonds : bond 0.21168 ( 781) hydrogen bonds : angle 7.97218 ( 2232) metal coordination : bond 0.37734 ( 5) Misc. bond : bond 0.04695 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 ASP cc_start: 0.8754 (m-30) cc_final: 0.8510 (m-30) REVERT: F 121 MET cc_start: 0.7984 (mtm) cc_final: 0.7667 (mpp) REVERT: F 152 MET cc_start: 0.7985 (tmm) cc_final: 0.7662 (tmm) REVERT: E 694 GLU cc_start: 0.7860 (mp0) cc_final: 0.7607 (mp0) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.9150 time to fit residues: 298.8517 Evaluate side-chains 244 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN B 56 ASN B 115 GLN C 56 ASN D 260 GLN E 452 GLN ** E 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.059552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.045722 restraints weight = 37284.459| |-----------------------------------------------------------------------------| r_work (start): 0.2424 rms_B_bonded: 1.86 r_work: 0.2318 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2207 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16999 Z= 0.202 Angle : 0.633 10.120 23341 Z= 0.328 Chirality : 0.043 0.219 2737 Planarity : 0.006 0.049 2783 Dihedral : 15.562 177.544 3152 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.30 % Allowed : 10.70 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 1962 helix: 0.98 (0.17), residues: 886 sheet: 0.53 (0.29), residues: 303 loop : -0.68 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 104 TYR 0.019 0.002 TYR E 463 PHE 0.018 0.002 PHE A 126 TRP 0.022 0.002 TRP E 659 HIS 0.007 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00454 (16993) covalent geometry : angle 0.63334 (23341) hydrogen bonds : bond 0.04986 ( 781) hydrogen bonds : angle 5.19038 ( 2232) metal coordination : bond 0.00696 ( 5) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: C 185 ASP cc_start: 0.8994 (m-30) cc_final: 0.8765 (m-30) REVERT: F 152 MET cc_start: 0.8109 (tmm) cc_final: 0.7798 (tmm) REVERT: E 188 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7944 (tm-30) REVERT: E 587 TRP cc_start: 0.9064 (OUTLIER) cc_final: 0.8737 (t-100) outliers start: 37 outliers final: 4 residues processed: 276 average time/residue: 0.8641 time to fit residues: 258.4517 Evaluate side-chains 255 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 249 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain E residue 587 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.0370 chunk 154 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 56 ASN F 221 GLN E 92 GLN E 455 ASN ** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 724 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.059821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.046137 restraints weight = 37375.686| |-----------------------------------------------------------------------------| r_work (start): 0.2430 rms_B_bonded: 1.77 r_work: 0.2322 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.652 16999 Z= 0.250 Angle : 0.606 9.397 23341 Z= 0.312 Chirality : 0.043 0.169 2737 Planarity : 0.005 0.046 2783 Dihedral : 15.411 176.559 3152 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.68 % Allowed : 13.94 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1962 helix: 1.35 (0.17), residues: 890 sheet: 0.43 (0.29), residues: 303 loop : -0.57 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 146 TYR 0.019 0.002 TYR E 59 PHE 0.016 0.002 PHE A 126 TRP 0.021 0.002 TRP E 659 HIS 0.008 0.001 HIS E 724 Details of bonding type rmsd covalent geometry : bond 0.00420 (16993) covalent geometry : angle 0.60570 (23341) hydrogen bonds : bond 0.04758 ( 781) hydrogen bonds : angle 5.01920 ( 2232) metal coordination : bond 0.29168 ( 5) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: C 99 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8928 (mttt) REVERT: C 185 ASP cc_start: 0.8964 (m-30) cc_final: 0.8739 (m-30) REVERT: D 104 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8680 (mtpp) REVERT: F 212 GLU cc_start: 0.7965 (mp0) cc_final: 0.7669 (mp0) REVERT: E 188 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7929 (tm-30) REVERT: E 250 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8348 (ttmm) REVERT: E 587 TRP cc_start: 0.9063 (OUTLIER) cc_final: 0.8700 (t-100) outliers start: 43 outliers final: 11 residues processed: 276 average time/residue: 0.8811 time to fit residues: 263.4540 Evaluate side-chains 252 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 775 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 93 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 175 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 179 optimal weight: 0.4980 chunk 193 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 56 ASN C 102 ASN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN F 221 GLN F 222 ASN F 374 GLN E 96 GLN E 455 ASN ** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 GLN E 593 ASN E 647 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.059660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.045879 restraints weight = 37108.363| |-----------------------------------------------------------------------------| r_work (start): 0.2425 rms_B_bonded: 1.80 r_work: 0.2319 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2209 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16999 Z= 0.187 Angle : 0.613 9.785 23341 Z= 0.315 Chirality : 0.043 0.157 2737 Planarity : 0.005 0.071 2783 Dihedral : 15.366 176.440 3152 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.86 % Allowed : 15.12 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1962 helix: 1.39 (0.17), residues: 898 sheet: 0.38 (0.29), residues: 302 loop : -0.58 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 166 TYR 0.020 0.002 TYR E 59 PHE 0.016 0.002 PHE E 521 TRP 0.020 0.002 TRP E 659 HIS 0.005 0.001 HIS E 724 Details of bonding type rmsd covalent geometry : bond 0.00425 (16993) covalent geometry : angle 0.61308 (23341) hydrogen bonds : bond 0.04559 ( 781) hydrogen bonds : angle 4.94163 ( 2232) metal coordination : bond 0.00600 ( 5) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: B 48 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: B 102 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7992 (p0) REVERT: B 112 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: B 226 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.6809 (ptm160) REVERT: F 134 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8728 (ttmt) REVERT: E 96 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: E 188 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7924 (tm-30) REVERT: E 587 TRP cc_start: 0.9061 (OUTLIER) cc_final: 0.8705 (t-100) outliers start: 46 outliers final: 13 residues processed: 275 average time/residue: 0.9073 time to fit residues: 269.4955 Evaluate side-chains 261 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 775 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 176 optimal weight: 0.0170 chunk 140 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 56 ASN F 147 GLN F 221 GLN E 96 GLN E 455 ASN ** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.059492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.045780 restraints weight = 36403.563| |-----------------------------------------------------------------------------| r_work (start): 0.2424 rms_B_bonded: 1.75 r_work: 0.2315 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2204 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16999 Z= 0.183 Angle : 0.616 9.545 23341 Z= 0.315 Chirality : 0.043 0.157 2737 Planarity : 0.005 0.070 2783 Dihedral : 15.342 176.529 3152 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.74 % Allowed : 15.93 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1962 helix: 1.48 (0.17), residues: 891 sheet: 0.30 (0.30), residues: 288 loop : -0.52 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 166 TYR 0.019 0.002 TYR E 59 PHE 0.016 0.002 PHE E 521 TRP 0.019 0.002 TRP E 659 HIS 0.006 0.001 HIS E 647 Details of bonding type rmsd covalent geometry : bond 0.00417 (16993) covalent geometry : angle 0.61641 (23341) hydrogen bonds : bond 0.04479 ( 781) hydrogen bonds : angle 4.90775 ( 2232) metal coordination : bond 0.00572 ( 5) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: B 102 ASN cc_start: 0.8338 (p0) cc_final: 0.8065 (p0) REVERT: B 112 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: B 226 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.6893 (ptm160) REVERT: D 104 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8803 (mtpp) REVERT: F 134 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8692 (ttmt) REVERT: E 188 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 587 TRP cc_start: 0.9045 (OUTLIER) cc_final: 0.8675 (t-100) outliers start: 44 outliers final: 13 residues processed: 268 average time/residue: 0.8988 time to fit residues: 260.3341 Evaluate side-chains 254 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 298 MET Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 775 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 121 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 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 115 GLN B 56 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN F 221 GLN F 222 ASN E 96 GLN E 455 ASN ** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.059256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.045460 restraints weight = 37075.140| |-----------------------------------------------------------------------------| r_work (start): 0.2412 rms_B_bonded: 1.79 r_work: 0.2306 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2198 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16999 Z= 0.202 Angle : 0.637 10.606 23341 Z= 0.326 Chirality : 0.043 0.157 2737 Planarity : 0.005 0.076 2783 Dihedral : 15.353 176.479 3152 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.86 % Allowed : 16.37 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1962 helix: 1.39 (0.17), residues: 894 sheet: 0.32 (0.30), residues: 286 loop : -0.61 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 166 TYR 0.020 0.002 TYR E 59 PHE 0.017 0.002 PHE E 521 TRP 0.020 0.002 TRP E 659 HIS 0.005 0.001 HIS E 647 Details of bonding type rmsd covalent geometry : bond 0.00464 (16993) covalent geometry : angle 0.63652 (23341) hydrogen bonds : bond 0.04648 ( 781) hydrogen bonds : angle 4.94578 ( 2232) metal coordination : bond 0.00592 ( 5) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: B 48 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: B 99 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8623 (mtpm) REVERT: B 102 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.7986 (p0) REVERT: B 112 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: B 226 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.6927 (ptm160) REVERT: D 104 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8769 (mtpp) REVERT: D 260 GLN cc_start: 0.8304 (mm110) cc_final: 0.5499 (pt0) REVERT: F 134 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8753 (ttmt) REVERT: E 188 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7913 (tm-30) REVERT: E 250 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8330 (tppp) REVERT: E 587 TRP cc_start: 0.9063 (OUTLIER) cc_final: 0.8712 (t-100) outliers start: 46 outliers final: 16 residues processed: 275 average time/residue: 0.8904 time to fit residues: 264.6029 Evaluate side-chains 261 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 775 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 4 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 167 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 56 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN F 221 GLN E 96 GLN E 455 ASN ** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.059342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.045527 restraints weight = 36699.997| |-----------------------------------------------------------------------------| r_work (start): 0.2420 rms_B_bonded: 1.76 r_work: 0.2312 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2203 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16999 Z= 0.195 Angle : 0.644 10.954 23341 Z= 0.329 Chirality : 0.044 0.158 2737 Planarity : 0.006 0.084 2783 Dihedral : 15.345 176.679 3152 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.61 % Allowed : 17.24 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1962 helix: 1.41 (0.17), residues: 889 sheet: 0.24 (0.30), residues: 288 loop : -0.57 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 166 TYR 0.019 0.002 TYR E 59 PHE 0.017 0.002 PHE E 521 TRP 0.020 0.002 TRP E 659 HIS 0.004 0.001 HIS E 647 Details of bonding type rmsd covalent geometry : bond 0.00447 (16993) covalent geometry : angle 0.64369 (23341) hydrogen bonds : bond 0.04586 ( 781) hydrogen bonds : angle 4.93751 ( 2232) metal coordination : bond 0.00562 ( 5) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: B 48 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: B 102 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.8010 (p0) REVERT: B 112 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: B 226 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.6891 (ptm160) REVERT: C 99 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8857 (mttm) REVERT: D 70 ASP cc_start: 0.8594 (m-30) cc_final: 0.8325 (m-30) REVERT: D 104 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8767 (mtpp) REVERT: D 260 GLN cc_start: 0.8299 (mm110) cc_final: 0.5492 (pt0) REVERT: F 120 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8378 (tt) REVERT: F 134 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8722 (ttmt) REVERT: E 188 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7905 (tm-30) REVERT: E 250 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8393 (tppp) REVERT: E 587 TRP cc_start: 0.9058 (OUTLIER) cc_final: 0.8711 (t-100) outliers start: 42 outliers final: 17 residues processed: 266 average time/residue: 0.8717 time to fit residues: 250.8144 Evaluate side-chains 271 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 775 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN F 147 GLN F 221 GLN F 222 ASN E 96 GLN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 ASN ** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.059759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.045978 restraints weight = 36558.876| |-----------------------------------------------------------------------------| r_work (start): 0.2428 rms_B_bonded: 1.70 r_work: 0.2319 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2208 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16999 Z= 0.182 Angle : 0.640 11.556 23341 Z= 0.325 Chirality : 0.043 0.159 2737 Planarity : 0.005 0.086 2783 Dihedral : 15.339 176.940 3152 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.80 % Allowed : 17.67 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1962 helix: 1.41 (0.17), residues: 898 sheet: 0.27 (0.30), residues: 286 loop : -0.60 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 166 TYR 0.019 0.002 TYR E 463 PHE 0.016 0.002 PHE E 521 TRP 0.019 0.002 TRP E 659 HIS 0.004 0.001 HIS E 393 Details of bonding type rmsd covalent geometry : bond 0.00416 (16993) covalent geometry : angle 0.63955 (23341) hydrogen bonds : bond 0.04438 ( 781) hydrogen bonds : angle 4.88094 ( 2232) metal coordination : bond 0.00562 ( 5) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: B 48 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: B 99 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8613 (mtpm) REVERT: B 102 ASN cc_start: 0.8368 (p0) cc_final: 0.8027 (p0) REVERT: B 112 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: B 226 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.6909 (ptm160) REVERT: C 99 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8852 (mttm) REVERT: C 185 ASP cc_start: 0.8837 (m-30) cc_final: 0.8624 (m-30) REVERT: D 70 ASP cc_start: 0.8543 (m-30) cc_final: 0.8339 (m-30) REVERT: D 104 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8801 (mtpp) REVERT: D 260 GLN cc_start: 0.8306 (mm110) cc_final: 0.5436 (pt0) REVERT: F 134 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8694 (ttmt) REVERT: E 124 MET cc_start: 0.8981 (tpp) cc_final: 0.8709 (ttp) REVERT: E 188 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7892 (tm-30) REVERT: E 250 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8432 (tppp) REVERT: E 587 TRP cc_start: 0.9052 (OUTLIER) cc_final: 0.8696 (t-100) outliers start: 45 outliers final: 19 residues processed: 269 average time/residue: 0.9088 time to fit residues: 263.8427 Evaluate side-chains 262 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 775 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 62 optimal weight: 0.0980 chunk 132 optimal weight: 2.9990 chunk 183 optimal weight: 0.0670 chunk 147 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 198 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN F 147 GLN F 221 GLN E 96 GLN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 ASN ** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN E 647 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.060464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.046809 restraints weight = 36641.260| |-----------------------------------------------------------------------------| r_work (start): 0.2450 rms_B_bonded: 1.73 r_work: 0.2342 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2231 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16999 Z= 0.159 Angle : 0.638 12.684 23341 Z= 0.322 Chirality : 0.042 0.157 2737 Planarity : 0.005 0.088 2783 Dihedral : 15.314 177.257 3152 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.24 % Allowed : 18.54 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1962 helix: 1.52 (0.17), residues: 892 sheet: 0.23 (0.29), residues: 304 loop : -0.55 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 166 TYR 0.020 0.002 TYR F 132 PHE 0.014 0.002 PHE A 126 TRP 0.018 0.002 TRP E 659 HIS 0.004 0.001 HIS E 393 Details of bonding type rmsd covalent geometry : bond 0.00362 (16993) covalent geometry : angle 0.63831 (23341) hydrogen bonds : bond 0.04152 ( 781) hydrogen bonds : angle 4.81416 ( 2232) metal coordination : bond 0.00496 ( 5) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: B 48 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: B 99 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8599 (mtpm) REVERT: B 102 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7999 (p0) REVERT: B 226 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.6864 (ptm160) REVERT: C 185 ASP cc_start: 0.8797 (m-30) cc_final: 0.8582 (m-30) REVERT: D 104 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8765 (mtpp) REVERT: D 260 GLN cc_start: 0.8303 (mm110) cc_final: 0.5437 (pt0) REVERT: F 134 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8661 (ttmt) REVERT: E 188 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7893 (tm-30) REVERT: E 250 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8445 (tppp) REVERT: E 462 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7971 (mm-30) REVERT: E 465 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7758 (mpp80) REVERT: E 587 TRP cc_start: 0.9037 (OUTLIER) cc_final: 0.8683 (t-100) REVERT: E 727 GLN cc_start: 0.6652 (tp-100) cc_final: 0.6313 (tp-100) outliers start: 36 outliers final: 15 residues processed: 264 average time/residue: 0.9006 time to fit residues: 256.2552 Evaluate side-chains 260 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 775 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 99 optimal weight: 0.0570 chunk 28 optimal weight: 0.5980 chunk 78 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 102 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN D 162 GLN F 147 GLN F 221 GLN F 222 ASN E 96 GLN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 ASN ** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS ** E 724 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 = 0.2822 r_free = 0.2822 target = 0.061624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.047947 restraints weight = 35993.520| |-----------------------------------------------------------------------------| r_work (start): 0.2485 rms_B_bonded: 1.68 r_work: 0.2382 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16999 Z= 0.132 Angle : 0.626 12.899 23341 Z= 0.314 Chirality : 0.042 0.154 2737 Planarity : 0.005 0.089 2783 Dihedral : 15.260 177.607 3152 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.87 % Allowed : 19.29 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1962 helix: 1.64 (0.17), residues: 891 sheet: 0.16 (0.30), residues: 304 loop : -0.47 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 166 TYR 0.017 0.002 TYR F 132 PHE 0.013 0.001 PHE A 126 TRP 0.017 0.001 TRP E 659 HIS 0.010 0.001 HIS E 724 Details of bonding type rmsd covalent geometry : bond 0.00298 (16993) covalent geometry : angle 0.62579 (23341) hydrogen bonds : bond 0.03747 ( 781) hydrogen bonds : angle 4.71388 ( 2232) metal coordination : bond 0.00684 ( 5) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: B 48 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: B 99 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8774 (mtpm) REVERT: B 102 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8014 (p0) REVERT: C 99 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8841 (mttm) REVERT: D 260 GLN cc_start: 0.8264 (mm110) cc_final: 0.5396 (pt0) REVERT: F 134 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8651 (ttmt) REVERT: E 96 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: E 188 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7877 (tm-30) REVERT: E 250 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8474 (tppp) REVERT: E 587 TRP cc_start: 0.9003 (OUTLIER) cc_final: 0.8522 (t-100) outliers start: 30 outliers final: 16 residues processed: 271 average time/residue: 0.9179 time to fit residues: 268.1952 Evaluate side-chains 254 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 775 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN F 147 GLN F 221 GLN F 222 ASN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 ASN E 647 HIS ** E 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.060419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.046563 restraints weight = 35829.794| |-----------------------------------------------------------------------------| r_work (start): 0.2446 rms_B_bonded: 1.73 r_work: 0.2339 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2227 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 16999 Z= 0.204 Angle : 0.682 13.014 23341 Z= 0.349 Chirality : 0.044 0.185 2737 Planarity : 0.006 0.089 2783 Dihedral : 15.253 177.257 3152 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.99 % Allowed : 20.10 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1962 helix: 1.54 (0.17), residues: 885 sheet: 0.29 (0.30), residues: 304 loop : -0.53 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 166 TYR 0.019 0.002 TYR E 59 PHE 0.016 0.002 PHE E 521 TRP 0.017 0.002 TRP E 659 HIS 0.008 0.001 HIS E 724 Details of bonding type rmsd covalent geometry : bond 0.00470 (16993) covalent geometry : angle 0.68213 (23341) hydrogen bonds : bond 0.04387 ( 781) hydrogen bonds : angle 4.84661 ( 2232) metal coordination : bond 0.01957 ( 5) Misc. bond : bond 0.00029 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7054.47 seconds wall clock time: 120 minutes 57.88 seconds (7257.88 seconds total)