Starting phenix.real_space_refine on Sat Jun 14 18:41:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey2_50052/06_2025/9ey2_50052.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey2_50052/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ey2_50052/06_2025/9ey2_50052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey2_50052/06_2025/9ey2_50052.map" model { file = "/net/cci-nas-00/data/ceres_data/9ey2_50052/06_2025/9ey2_50052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey2_50052/06_2025/9ey2_50052.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.31, per 1000 atoms: 0.80 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: 4.63 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 6.56 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: 6.37 Time building geometry restraints manager: 5.46 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: 0.000 Normalize map: mean=0, sd=1: 14.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 52.710 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.090 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:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.059 0.008 TRP E 659 HIS 0.051 0.006 HIS E 724 PHE 0.057 0.008 PHE B 159 TYR 0.051 0.006 TYR E 59 ARG 0.031 0.003 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.21168 ( 781) hydrogen bonds : angle 7.97218 ( 2232) metal coordination : bond 0.37734 ( 5) covalent geometry : bond 0.00910 (16993) covalent geometry : angle 1.16600 (23341) 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 : 1.875 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: 0.7663 (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: 1.7803 time to fit residues: 583.0853 Evaluate side-chains 243 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 157 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.2775 r_free = 0.2775 target = 0.059768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.045953 restraints weight = 37533.898| |-----------------------------------------------------------------------------| r_work (start): 0.2430 rms_B_bonded: 1.80 r_work: 0.2325 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2218 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16999 Z= 0.190 Angle : 0.628 10.359 23341 Z= 0.324 Chirality : 0.043 0.223 2737 Planarity : 0.006 0.048 2783 Dihedral : 15.557 177.523 3152 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.24 % Allowed : 10.70 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 1962 helix: 0.99 (0.17), residues: 886 sheet: 0.53 (0.29), residues: 303 loop : -0.66 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 659 HIS 0.007 0.001 HIS F 242 PHE 0.017 0.002 PHE A 126 TYR 0.020 0.002 TYR E 463 ARG 0.009 0.001 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 781) hydrogen bonds : angle 5.17876 ( 2232) metal coordination : bond 0.01138 ( 5) covalent geometry : bond 0.00424 (16993) covalent geometry : angle 0.62753 (23341) Misc. bond : bond 0.00017 ( 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 302 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: C 185 ASP cc_start: 0.8979 (m-30) cc_final: 0.8771 (m-30) REVERT: F 152 MET cc_start: 0.8060 (tmm) cc_final: 0.7688 (tmm) REVERT: E 188 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7874 (tm-30) REVERT: E 587 TRP cc_start: 0.9057 (OUTLIER) cc_final: 0.8727 (t-100) outliers start: 36 outliers final: 4 residues processed: 272 average time/residue: 1.8262 time to fit residues: 539.8696 Evaluate side-chains 254 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 248 time to evaluate : 1.759 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 188 optimal weight: 1.9990 chunk 186 optimal weight: 0.0970 chunk 187 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 E 92 GLN ** E 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.060012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.046412 restraints weight = 37450.469| |-----------------------------------------------------------------------------| r_work (start): 0.2443 rms_B_bonded: 1.65 r_work: 0.2338 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2227 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16999 Z= 0.166 Angle : 0.586 8.886 23341 Z= 0.301 Chirality : 0.042 0.170 2737 Planarity : 0.005 0.053 2783 Dihedral : 15.370 176.880 3152 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.43 % Allowed : 13.44 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 1962 helix: 1.41 (0.17), residues: 891 sheet: 0.42 (0.29), residues: 303 loop : -0.51 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 659 HIS 0.006 0.001 HIS F 242 PHE 0.015 0.002 PHE E 521 TYR 0.018 0.002 TYR E 59 ARG 0.009 0.001 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 781) hydrogen bonds : angle 4.95161 ( 2232) metal coordination : bond 0.00436 ( 5) covalent geometry : bond 0.00372 (16993) covalent geometry : angle 0.58561 (23341) Misc. bond : bond 0.00024 ( 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 297 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: B 226 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.6900 (ptm160) REVERT: C 99 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8857 (mttm) REVERT: D 104 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8646 (mtpp) REVERT: E 188 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 250 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8360 (ttmm) REVERT: E 587 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.8619 (t-100) outliers start: 39 outliers final: 9 residues processed: 274 average time/residue: 2.0358 time to fit residues: 606.5726 Evaluate side-chains 250 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 1.791 ------------------------------------------------------------------------------- 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 226 ARG 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 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 57 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 138 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 F 222 ASN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN E 455 ASN E 647 HIS E 724 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.060400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.046755 restraints weight = 36922.141| |-----------------------------------------------------------------------------| r_work (start): 0.2447 rms_B_bonded: 1.70 r_work: 0.2341 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2232 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.589 16999 Z= 0.222 Angle : 0.596 9.449 23341 Z= 0.306 Chirality : 0.042 0.155 2737 Planarity : 0.005 0.060 2783 Dihedral : 15.326 176.822 3152 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.55 % Allowed : 14.62 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 1962 helix: 1.46 (0.17), residues: 898 sheet: 0.38 (0.29), residues: 302 loop : -0.51 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 659 HIS 0.013 0.001 HIS E 724 PHE 0.015 0.002 PHE E 521 TYR 0.018 0.002 TYR E 59 ARG 0.009 0.001 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 781) hydrogen bonds : angle 4.87747 ( 2232) metal coordination : bond 0.26346 ( 5) covalent geometry : bond 0.00369 (16993) covalent geometry : angle 0.59635 (23341) Misc. bond : bond 0.00011 ( 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 296 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: B 48 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: B 226 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.6926 (ptm160) REVERT: C 99 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8857 (mttm) REVERT: E 188 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7870 (tm-30) REVERT: E 250 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8358 (ttmm) REVERT: E 587 TRP cc_start: 0.9039 (OUTLIER) cc_final: 0.8679 (t-100) outliers start: 41 outliers final: 11 residues processed: 270 average time/residue: 1.8035 time to fit residues: 529.0882 Evaluate side-chains 252 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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 107 GLN Chi-restraints excluded: chain B residue 206 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 20 optimal weight: 0.0570 chunk 196 optimal weight: 0.0050 overall best weight: 0.4512 ------------------------------------------------------------------------------- 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 F 263 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 589 GLN E 593 ASN E 647 HIS E 727 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.060638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.046830 restraints weight = 36856.813| |-----------------------------------------------------------------------------| r_work (start): 0.2455 rms_B_bonded: 1.72 r_work: 0.2348 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2240 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16999 Z= 0.150 Angle : 0.586 9.751 23341 Z= 0.299 Chirality : 0.042 0.153 2737 Planarity : 0.005 0.062 2783 Dihedral : 15.276 176.965 3152 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.61 % Allowed : 15.56 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1962 helix: 1.54 (0.17), residues: 897 sheet: 0.34 (0.29), residues: 302 loop : -0.45 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 659 HIS 0.005 0.001 HIS E 647 PHE 0.014 0.002 PHE E 521 TYR 0.019 0.002 TYR E 463 ARG 0.010 0.001 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 781) hydrogen bonds : angle 4.80622 ( 2232) metal coordination : bond 0.00364 ( 5) covalent geometry : bond 0.00337 (16993) covalent geometry : angle 0.58604 (23341) Misc. bond : bond 0.00012 ( 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 300 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8248 (ttp) REVERT: A 232 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: B 48 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: B 226 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.6921 (ptm160) REVERT: B 229 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8424 (t0) REVERT: C 99 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8870 (mttm) REVERT: C 185 ASP cc_start: 0.8915 (m-30) cc_final: 0.8712 (m-30) REVERT: D 104 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8745 (mtpp) REVERT: D 260 GLN cc_start: 0.8256 (mm110) cc_final: 0.5485 (pt0) REVERT: E 188 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7867 (tm-30) REVERT: E 250 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8364 (ttmm) REVERT: E 587 TRP cc_start: 0.9023 (OUTLIER) cc_final: 0.8604 (t-100) outliers start: 42 outliers final: 12 residues processed: 277 average time/residue: 2.0665 time to fit residues: 621.2939 Evaluate side-chains 255 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 2.489 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain C residue 99 LYS 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 120 LEU Chi-restraints excluded: chain F residue 213 ASN 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 104 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN F 221 GLN F 222 ASN E 96 GLN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 GLN E 455 ASN ** E 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.059230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.045481 restraints weight = 36912.577| |-----------------------------------------------------------------------------| r_work (start): 0.2411 rms_B_bonded: 1.77 r_work: 0.2302 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2191 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16999 Z= 0.214 Angle : 0.649 11.026 23341 Z= 0.332 Chirality : 0.044 0.155 2737 Planarity : 0.005 0.073 2783 Dihedral : 15.340 176.323 3152 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.80 % Allowed : 16.37 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1962 helix: 1.43 (0.17), residues: 897 sheet: 0.31 (0.30), residues: 286 loop : -0.55 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 659 HIS 0.005 0.001 HIS E 647 PHE 0.018 0.002 PHE E 521 TYR 0.021 0.002 TYR E 59 ARG 0.010 0.001 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 781) hydrogen bonds : angle 4.95793 ( 2232) metal coordination : bond 0.00557 ( 5) covalent geometry : bond 0.00492 (16993) covalent geometry : angle 0.64905 (23341) Misc. bond : bond 0.00022 ( 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 299 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9024 (tp) cc_final: 0.8812 (tt) REVERT: A 147 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8612 (mtm180) REVERT: B 48 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: B 226 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.6925 (ptm160) REVERT: C 99 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8846 (mttm) REVERT: C 185 ASP cc_start: 0.8960 (m-30) cc_final: 0.8744 (m-30) REVERT: D 104 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8797 (mtpp) REVERT: F 134 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8686 (ttmt) REVERT: E 113 MET cc_start: 0.9065 (tpt) cc_final: 0.8850 (tpp) REVERT: E 188 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7885 (tm-30) REVERT: E 587 TRP cc_start: 0.9063 (OUTLIER) cc_final: 0.8756 (t-100) outliers start: 45 outliers final: 14 residues processed: 276 average time/residue: 1.9438 time to fit residues: 584.4257 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 : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 147 ARG 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 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 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 299 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 69 ASP 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 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 141 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.059528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.045721 restraints weight = 36877.907| |-----------------------------------------------------------------------------| r_work (start): 0.2422 rms_B_bonded: 1.69 r_work: 0.2315 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2203 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16999 Z= 0.196 Angle : 0.643 10.928 23341 Z= 0.328 Chirality : 0.043 0.157 2737 Planarity : 0.005 0.079 2783 Dihedral : 15.330 176.699 3152 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.36 % Allowed : 17.24 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1962 helix: 1.42 (0.17), residues: 897 sheet: 0.27 (0.30), residues: 286 loop : -0.59 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 659 HIS 0.004 0.001 HIS E 647 PHE 0.017 0.002 PHE E 521 TYR 0.020 0.002 TYR E 463 ARG 0.011 0.001 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 781) hydrogen bonds : angle 4.92500 ( 2232) metal coordination : bond 0.00475 ( 5) covalent geometry : bond 0.00448 (16993) covalent geometry : angle 0.64306 (23341) Misc. bond : bond 0.00042 ( 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 291 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8449 (mtm180) REVERT: A 232 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: B 48 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: B 226 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.6845 (ptm160) REVERT: C 99 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8856 (mttm) REVERT: D 70 ASP cc_start: 0.8583 (m-30) cc_final: 0.8337 (m-30) REVERT: D 104 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8769 (mtpp) REVERT: D 260 GLN cc_start: 0.8302 (mm110) cc_final: 0.5539 (pt0) REVERT: F 134 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8711 (ttmt) REVERT: E 188 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7937 (tm-30) REVERT: E 250 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8171 (ttmm) REVERT: E 587 TRP cc_start: 0.9064 (OUTLIER) cc_final: 0.8711 (t-100) outliers start: 38 outliers final: 15 residues processed: 272 average time/residue: 1.8585 time to fit residues: 551.2312 Evaluate side-chains 266 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 147 ARG 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 107 GLN 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 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 299 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 673 LEU 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 166 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 194 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 189 optimal weight: 0.0570 chunk 157 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.059898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.046154 restraints weight = 36804.071| |-----------------------------------------------------------------------------| r_work (start): 0.2437 rms_B_bonded: 1.68 r_work: 0.2329 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2219 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16999 Z= 0.174 Angle : 0.636 11.505 23341 Z= 0.324 Chirality : 0.043 0.157 2737 Planarity : 0.005 0.084 2783 Dihedral : 15.327 176.982 3152 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.61 % Allowed : 17.42 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 1962 helix: 1.46 (0.17), residues: 898 sheet: 0.25 (0.30), residues: 286 loop : -0.55 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 659 HIS 0.004 0.001 HIS E 393 PHE 0.015 0.002 PHE E 521 TYR 0.020 0.002 TYR E 463 ARG 0.012 0.001 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 781) hydrogen bonds : angle 4.86751 ( 2232) metal coordination : bond 0.00430 ( 5) covalent geometry : bond 0.00398 (16993) covalent geometry : angle 0.63562 (23341) Misc. bond : bond 0.00008 ( 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 294 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8590 (mtm180) REVERT: A 232 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: B 48 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: B 226 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.6829 (ptm160) REVERT: C 99 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8867 (mttm) REVERT: D 104 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8774 (mtpp) REVERT: D 260 GLN cc_start: 0.8273 (mm110) cc_final: 0.5510 (pt0) REVERT: F 134 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8710 (ttmt) REVERT: E 96 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: E 188 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7928 (tm-30) REVERT: E 250 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8157 (ttmm) REVERT: E 587 TRP cc_start: 0.9054 (OUTLIER) cc_final: 0.8715 (t-100) REVERT: E 727 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6765 (tp-100) outliers start: 42 outliers final: 16 residues processed: 276 average time/residue: 1.7540 time to fit residues: 524.6521 Evaluate side-chains 264 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 147 ARG 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 107 GLN 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 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 299 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 GLN 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 170 optimal weight: 0.3980 chunk 43 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 157 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 94 optimal weight: 0.0980 chunk 149 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 190 optimal weight: 0.0050 chunk 24 optimal weight: 0.7980 overall best weight: 0.2192 ------------------------------------------------------------------------------- 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 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 = 0.2831 r_free = 0.2831 target = 0.062008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.048261 restraints weight = 36954.793| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 1.66 r_work: 0.2392 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2285 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16999 Z= 0.123 Angle : 0.606 12.207 23341 Z= 0.304 Chirality : 0.041 0.152 2737 Planarity : 0.005 0.086 2783 Dihedral : 15.274 177.722 3152 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.49 % Allowed : 18.73 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1962 helix: 1.62 (0.17), residues: 898 sheet: 0.22 (0.29), residues: 302 loop : -0.46 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 659 HIS 0.005 0.001 HIS E 98 PHE 0.012 0.001 PHE A 126 TYR 0.017 0.002 TYR E 463 ARG 0.013 0.000 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 781) hydrogen bonds : angle 4.70591 ( 2232) metal coordination : bond 0.00370 ( 5) covalent geometry : bond 0.00276 (16993) covalent geometry : angle 0.60624 (23341) Misc. bond : bond 0.00017 ( 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 287 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: B 48 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: B 229 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8418 (t0) REVERT: C 99 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8845 (mttm) REVERT: C 185 ASP cc_start: 0.8856 (m-30) cc_final: 0.8636 (m-30) REVERT: D 70 ASP cc_start: 0.8508 (m-30) cc_final: 0.8171 (m-30) REVERT: D 260 GLN cc_start: 0.8243 (mm110) cc_final: 0.5490 (pt0) REVERT: E 96 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: E 188 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7870 (tm-30) REVERT: E 461 GLN cc_start: 0.8579 (mt0) cc_final: 0.7957 (mt0) REVERT: E 462 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7984 (mm-30) REVERT: E 587 TRP cc_start: 0.9001 (OUTLIER) cc_final: 0.8476 (t-100) outliers start: 24 outliers final: 9 residues processed: 275 average time/residue: 1.7189 time to fit residues: 513.0063 Evaluate side-chains 257 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 226 ARG Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain F residue 113 THR 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 438 ILE Chi-restraints excluded: chain E residue 587 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 47 optimal weight: 0.0570 chunk 161 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 170 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 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 457 GLN E 647 HIS ** E 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.060835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.046985 restraints weight = 36077.905| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 1.69 r_work: 0.2353 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2246 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16999 Z= 0.163 Angle : 0.649 12.826 23341 Z= 0.327 Chirality : 0.043 0.188 2737 Planarity : 0.005 0.091 2783 Dihedral : 15.260 177.249 3152 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.15 % Rotamer: Outliers : 1.43 % Allowed : 19.85 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1962 helix: 1.55 (0.17), residues: 897 sheet: 0.28 (0.30), residues: 302 loop : -0.47 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 659 HIS 0.008 0.001 HIS E 724 PHE 0.034 0.002 PHE E 735 TYR 0.023 0.002 TYR F 132 ARG 0.014 0.001 ARG E 465 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 781) hydrogen bonds : angle 4.77836 ( 2232) metal coordination : bond 0.01478 ( 5) covalent geometry : bond 0.00373 (16993) covalent geometry : angle 0.64930 (23341) Misc. bond : bond 0.00004 ( 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 271 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: B 48 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: C 99 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8840 (mttm) REVERT: C 185 ASP cc_start: 0.8884 (m-30) cc_final: 0.8673 (m-30) REVERT: D 70 ASP cc_start: 0.8508 (m-30) cc_final: 0.7998 (m-30) REVERT: D 260 GLN cc_start: 0.8286 (mm110) cc_final: 0.5427 (pt0) REVERT: E 188 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7866 (tm-30) REVERT: E 250 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8377 (tppp) REVERT: E 494 MET cc_start: 0.6528 (tpp) cc_final: 0.5997 (tpp) REVERT: E 587 TRP cc_start: 0.9025 (OUTLIER) cc_final: 0.8661 (t-100) outliers start: 23 outliers final: 10 residues processed: 262 average time/residue: 1.8869 time to fit residues: 535.7616 Evaluate side-chains 250 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 213 ASN Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 438 ILE 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 42 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 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 B 56 ASN F 147 GLN F 221 GLN F 222 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.059762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.045786 restraints weight = 36556.654| |-----------------------------------------------------------------------------| r_work (start): 0.2423 rms_B_bonded: 1.74 r_work: 0.2318 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2208 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16999 Z= 0.202 Angle : 0.684 12.723 23341 Z= 0.346 Chirality : 0.044 0.151 2737 Planarity : 0.006 0.092 2783 Dihedral : 15.309 176.979 3152 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.62 % Allowed : 19.73 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1962 helix: 1.44 (0.17), residues: 892 sheet: 0.21 (0.30), residues: 304 loop : -0.55 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 659 HIS 0.007 0.001 HIS E 724 PHE 0.016 0.002 PHE E 521 TYR 0.022 0.002 TYR F 132 ARG 0.014 0.001 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 781) hydrogen bonds : angle 4.92239 ( 2232) metal coordination : bond 0.01879 ( 5) covalent geometry : bond 0.00466 (16993) covalent geometry : angle 0.68427 (23341) Misc. bond : bond 0.00067 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15044.35 seconds wall clock time: 262 minutes 16.71 seconds (15736.71 seconds total)