Starting phenix.real_space_refine on Thu Aug 6 17:57:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey0_50050/08_2026/9ey0_50050.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey0_50050/08_2026/9ey0_50050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ey0_50050/08_2026/9ey0_50050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey0_50050/08_2026/9ey0_50050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ey0_50050/08_2026/9ey0_50050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey0_50050/08_2026/9ey0_50050.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 68 5.49 5 S 86 5.16 5 C 10302 2.51 5 N 2937 2.21 5 O 3296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16691 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: "E" Number of atoms: 5508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5508 Classifications: {'peptide': 704} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 659} Chain breaks: 2 Chain: "T" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1375 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna2p': 15, 'rna3p': 49} Chain breaks: 1 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: "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} 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: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 3.20, per 1000 atoms: 0.19 Number of scatterers: 16691 At special positions: 0 Unit cell: (103.02, 117.16, 170.69, 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 86 16.00 P 68 15.00 O 3296 8.00 N 2937 7.00 C 10302 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: 1.33 Conformation dependent library (CDL) restraints added in 679.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 546 " pdb="ZN ZN E 901 " - pdb=" ND1 HIS E 548 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 644 " pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 551 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 724 " 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 15 sheets defined 50.5% alpha, 12.8% beta 16 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.746A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.552A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.544A 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 Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.529A pdb=" N LEU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.764A 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 122 removed outlier: 3.993A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 139 removed outlier: 3.631A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.570A 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 221 removed outlier: 3.775A pdb=" N PHE B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 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 122 Processing helix chain 'C' and resid 122 through 137 removed outlier: 3.990A pdb=" N GLY C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.791A 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: 3.834A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.509A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.724A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 removed outlier: 3.522A pdb=" N VAL D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.644A pdb=" N GLY D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.707A 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 209 removed outlier: 3.697A pdb=" N LEU D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 removed outlier: 3.637A pdb=" N VAL D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'E' and resid 37 through 47 removed outlier: 4.031A pdb=" N ARG E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 98 Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.542A pdb=" N GLU E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 263 removed outlier: 3.503A pdb=" N ALA E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 270 Processing helix chain 'E' and resid 271 through 280 removed outlier: 4.233A pdb=" N ALA E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA E 277 " --> pdb=" O PRO E 273 " (cutoff:3.500A) 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 331 removed outlier: 3.702A pdb=" N GLN E 327 " --> pdb=" O ASN E 323 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN E 330 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY E 331 " --> pdb=" O GLN E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 323 through 331' Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 351 through 361 removed outlier: 3.773A pdb=" N PHE E 361 " --> pdb=" O TRP E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 393 removed outlier: 3.567A pdb=" N LEU E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE E 392 " --> pdb=" O GLN E 388 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 removed outlier: 4.176A pdb=" N PHE E 446 " --> pdb=" O ASN E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 519 through 529 Processing helix chain 'E' and resid 531 through 538 Processing helix chain 'E' and resid 548 through 553 removed outlier: 3.613A pdb=" N HIS E 552 " --> pdb=" O HIS E 548 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E 553 " --> pdb=" O ALA E 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 548 through 553' Processing helix chain 'E' and resid 554 through 570 removed outlier: 3.507A pdb=" N ILE E 558 " --> pdb=" O GLY E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 595 removed outlier: 3.906A pdb=" N TRP E 587 " --> pdb=" O GLN E 583 " (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 618 through 633 Processing helix chain 'E' and resid 670 through 677 removed outlier: 3.671A pdb=" N VAL E 674 " --> pdb=" O CYS E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 701 removed outlier: 3.512A pdb=" N GLU E 699 " --> pdb=" O GLU E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 716 Processing helix chain 'E' and resid 755 through 762 Proline residue: E 758 - end of helix Proline residue: E 761 - end of helix No H-bonds generated for 'chain 'E' and resid 755 through 762' Processing helix chain 'E' and resid 763 through 771 Processing helix chain 'E' and resid 771 through 791 removed outlier: 4.112A pdb=" N GLU E 779 " --> pdb=" O ILE E 775 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU E 780 " --> pdb=" O GLU E 776 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG E 781 " --> pdb=" O GLU E 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.565A pdb=" N THR F 119 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS F 123 " --> pdb=" O THR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 164 removed outlier: 3.535A pdb=" N LYS F 153 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.692A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 removed outlier: 3.650A pdb=" N MET F 215 " --> pdb=" O GLU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 237 Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 removed outlier: 3.742A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 269 " --> pdb=" O TRP F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 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 removed outlier: 3.630A pdb=" N LEU F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.681A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.459A 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 60 removed outlier: 6.274A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.438A 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 60 removed outlier: 6.290A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ILE C 251 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR C 195 " --> pdb=" O ILE C 251 " (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: 6.507A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (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 'E' and resid 162 through 167 removed outlier: 6.621A pdb=" N CYS E 136 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG E 166 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU E 138 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE E 108 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG E 82 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N PHE E 109 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU E 84 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA E 73 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL E 63 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL E 58 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 432 " --> pdb=" O GLN E 426 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.657A pdb=" N TYR E 173 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL E 241 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU E 310 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA E 305 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL E 341 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 307 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N MET E 343 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL E 309 " --> pdb=" O MET E 343 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N HIS E 367 " --> pdb=" O VAL E 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AB3, first strand: chain 'E' and resid 602 through 606 removed outlier: 5.919A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA E 540 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL E 579 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL E 542 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER E 511 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL E 542 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 513 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR E 510 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET E 750 " --> pdb=" O PHE E 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 634 through 638 removed outlier: 6.121A pdb=" N LEU E 683 " --> pdb=" O MET E 721 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN E 723 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N HIS E 685 " --> pdb=" O ASN E 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 272 through 273 removed outlier: 8.371A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 342 through 344 removed outlier: 5.488A pdb=" N GLN F 343 " --> pdb=" O THR F 382 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2686 1.31 - 1.44: 4536 1.44 - 1.57: 9634 1.57 - 1.69: 135 1.69 - 1.82: 138 Bond restraints: 17129 Sorted by residual: bond pdb=" C2' GTP T 101 " pdb=" C3' GTP T 101 " ideal model delta sigma weight residual 1.524 1.238 0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C1' GTP T 101 " pdb=" N9 GTP T 101 " ideal model delta sigma weight residual 1.475 1.320 0.155 2.00e-02 2.50e+03 6.01e+01 bond pdb=" CA PHE F 97 " pdb=" C PHE F 97 " ideal model delta sigma weight residual 1.523 1.624 -0.101 1.35e-02 5.49e+03 5.59e+01 bond pdb=" C3' GTP T 101 " pdb=" C4' GTP T 101 " ideal model delta sigma weight residual 1.524 1.661 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C5 GTP T 101 " pdb=" C6 GTP T 101 " ideal model delta sigma weight residual 1.390 1.525 -0.135 2.00e-02 2.50e+03 4.57e+01 ... (remaining 17124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 23285 2.66 - 5.31: 197 5.31 - 7.97: 21 7.97 - 10.63: 6 10.63 - 13.29: 1 Bond angle restraints: 23510 Sorted by residual: angle pdb=" N ILE F 98 " pdb=" CA ILE F 98 " pdb=" C ILE F 98 " ideal model delta sigma weight residual 110.62 123.91 -13.29 1.02e+00 9.61e-01 1.70e+02 angle pdb=" N VAL D 213 " pdb=" CA VAL D 213 " pdb=" C VAL D 213 " ideal model delta sigma weight residual 110.42 118.94 -8.52 9.60e-01 1.09e+00 7.87e+01 angle pdb=" N GLU F 96 " pdb=" CA GLU F 96 " pdb=" C GLU F 96 " ideal model delta sigma weight residual 112.23 101.87 10.36 1.26e+00 6.30e-01 6.76e+01 angle pdb=" N ILE F 98 " pdb=" CA ILE F 98 " pdb=" CB ILE F 98 " ideal model delta sigma weight residual 110.54 102.69 7.85 1.36e+00 5.41e-01 3.33e+01 angle pdb=" CA PHE F 97 " pdb=" C PHE F 97 " pdb=" N ILE F 98 " ideal model delta sigma weight residual 117.22 110.57 6.65 1.17e+00 7.31e-01 3.23e+01 ... (remaining 23505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 9983 35.15 - 70.30: 401 70.30 - 105.46: 49 105.46 - 140.61: 3 140.61 - 175.76: 2 Dihedral angle restraints: 10438 sinusoidal: 4742 harmonic: 5696 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 -128.00 46.84 -174.84 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O2G GTP T 101 " pdb=" O3B GTP T 101 " pdb=" PG GTP T 101 " pdb=" PB GTP T 101 " ideal model delta sinusoidal sigma weight residual 177.30 -6.94 -175.76 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3B GTP T 101 " pdb=" O3A GTP T 101 " pdb=" PB GTP T 101 " pdb=" PA GTP T 101 " ideal model delta sinusoidal sigma weight residual -68.92 43.19 -112.12 1 2.00e+01 2.50e-03 3.30e+01 ... (remaining 10435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2396 0.065 - 0.130: 339 0.130 - 0.195: 10 0.195 - 0.259: 3 0.259 - 0.324: 1 Chirality restraints: 2749 Sorted by residual: chirality pdb=" CA PHE F 97 " pdb=" N PHE F 97 " pdb=" C PHE F 97 " pdb=" CB PHE F 97 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C2' SAM F 501 " pdb=" C1' SAM F 501 " pdb=" C3' SAM F 501 " pdb=" O2' SAM F 501 " both_signs ideal model delta sigma weight residual False -2.76 -2.52 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE F 98 " pdb=" N ILE F 98 " pdb=" C ILE F 98 " pdb=" CB ILE F 98 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2746 not shown) Planarity restraints: 2817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 97 " -0.011 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C PHE F 97 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE F 97 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE F 98 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 180 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO C 181 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 776 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" CD GLU E 776 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU E 776 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU E 776 " -0.007 2.00e-02 2.50e+03 ... (remaining 2814 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 178 2.58 - 3.16: 13911 3.16 - 3.74: 27308 3.74 - 4.32: 39055 4.32 - 4.90: 63427 Nonbonded interactions: 143879 Sorted by model distance: nonbonded pdb=" OD2 ASP E 550 " pdb="ZN ZN E 902 " model vdw 1.995 2.230 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 902 " model vdw 1.996 2.230 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 901 " model vdw 2.004 2.230 nonbonded pdb=" O ALA E 549 " pdb=" OG1 THR E 553 " model vdw 2.066 3.040 nonbonded pdb=" OG1 THR E 285 " pdb=" OE1 GLU E 290 " model vdw 2.072 3.040 ... (remaining 143874 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: 4.120 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 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 : 0.006 0.286 17135 Z= 0.274 Angle : 0.584 13.287 23510 Z= 0.342 Chirality : 0.043 0.324 2749 Planarity : 0.003 0.037 2817 Dihedral : 17.624 175.758 6778 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.18 % Allowed : 18.66 % Favored : 81.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1990 helix: 2.22 (0.18), residues: 868 sheet: -0.09 (0.29), residues: 365 loop : 0.36 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 430 TYR 0.008 0.001 TYR D 101 PHE 0.007 0.001 PHE F 312 TRP 0.004 0.001 TRP E 659 HIS 0.002 0.000 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (17129) covalent geometry : angle 0.58396 / 0.34 (23510) hydrogen bonds : bond 0.22334 / 15.35 ( 775) hydrogen bonds : angle 8.07919 / 5.94 ( 2203) metal coordination : bond 0.26388 / 16.23 ( 5) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8390 (mm-30) REVERT: C 70 ASP cc_start: 0.8537 (m-30) cc_final: 0.8316 (m-30) REVERT: D 179 THR cc_start: 0.9073 (t) cc_final: 0.8812 (m) REVERT: D 212 LYS cc_start: 0.8543 (tttp) cc_final: 0.7361 (tmtt) outliers start: 3 outliers final: 0 residues processed: 191 average time/residue: 0.5499 time to fit residues: 117.3096 Evaluate side-chains 159 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 ASN B 220 GLN D 102 ASN E 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.079402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059806 restraints weight = 35623.358| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.02 r_work: 0.2836 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17135 Z= 0.166 Angle : 0.591 7.772 23510 Z= 0.303 Chirality : 0.043 0.188 2749 Planarity : 0.005 0.056 2817 Dihedral : 13.590 177.871 3139 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.21 % Allowed : 17.80 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 1990 helix: 1.90 (0.18), residues: 875 sheet: -0.23 (0.29), residues: 345 loop : 0.26 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 43 TYR 0.013 0.001 TYR E 59 PHE 0.019 0.001 PHE F 97 TRP 0.011 0.001 TRP E 587 HIS 0.013 0.001 HIS E 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (17129) covalent geometry : angle 0.59080 / 0.30 (23510) hydrogen bonds : bond 0.05680 / 4.01 ( 775) hydrogen bonds : angle 5.79136 / 4.29 ( 2203) metal coordination : bond 0.01833 / 1.17 ( 5) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 70 ASP cc_start: 0.8688 (m-30) cc_final: 0.8447 (m-30) REVERT: D 179 THR cc_start: 0.9141 (t) cc_final: 0.8879 (m) REVERT: D 211 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7776 (tm-30) REVERT: E 162 GLU cc_start: 0.8053 (tp30) cc_final: 0.7813 (tp30) REVERT: E 412 LEU cc_start: 0.7637 (pt) cc_final: 0.7369 (mp) REVERT: E 713 MET cc_start: 0.8759 (mmm) cc_final: 0.8500 (mmm) REVERT: E 729 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8563 (m-80) REVERT: F 161 LYS cc_start: 0.8918 (tmmm) cc_final: 0.8647 (ptmm) outliers start: 36 outliers final: 10 residues processed: 224 average time/residue: 0.5554 time to fit residues: 138.4028 Evaluate side-chains 174 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 22 optimal weight: 0.3980 chunk 115 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 172 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 111 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN E 393 HIS E 527 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.079476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059668 restraints weight = 36571.720| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.06 r_work: 0.2831 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17135 Z= 0.135 Angle : 0.539 7.595 23510 Z= 0.274 Chirality : 0.041 0.154 2749 Planarity : 0.004 0.040 2817 Dihedral : 13.621 178.110 3139 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.58 % Allowed : 18.72 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 1990 helix: 1.93 (0.18), residues: 850 sheet: -0.19 (0.28), residues: 338 loop : 0.24 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 46 TYR 0.014 0.001 TYR E 59 PHE 0.012 0.001 PHE E 521 TRP 0.011 0.001 TRP E 587 HIS 0.004 0.001 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (17129) covalent geometry : angle 0.53877 / 0.27 (23510) hydrogen bonds : bond 0.04525 / 3.19 ( 775) hydrogen bonds : angle 5.30909 / 3.93 ( 2203) metal coordination : bond 0.00740 / 0.52 ( 5) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8654 (tptt) REVERT: A 206 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8558 (tp) REVERT: B 64 ASP cc_start: 0.8768 (t0) cc_final: 0.8516 (t0) REVERT: B 143 GLN cc_start: 0.8778 (pm20) cc_final: 0.8573 (pm20) REVERT: C 64 ASP cc_start: 0.8877 (t0) cc_final: 0.8525 (t0) REVERT: D 160 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: D 179 THR cc_start: 0.9083 (t) cc_final: 0.8822 (m) REVERT: E 162 GLU cc_start: 0.8090 (tp30) cc_final: 0.7881 (tp30) REVERT: E 412 LEU cc_start: 0.7738 (pt) cc_final: 0.7537 (mp) REVERT: E 608 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9183 (ttpp) REVERT: E 729 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8548 (m-80) REVERT: E 777 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8539 (tm-30) REVERT: F 99 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8831 (mm-30) REVERT: F 161 LYS cc_start: 0.8793 (tmmm) cc_final: 0.8523 (ptmm) outliers start: 42 outliers final: 11 residues processed: 223 average time/residue: 0.5672 time to fit residues: 141.1945 Evaluate side-chains 180 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 128 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 137 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058007 restraints weight = 36380.695| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.04 r_work: 0.2792 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17135 Z= 0.215 Angle : 0.588 7.648 23510 Z= 0.297 Chirality : 0.043 0.158 2749 Planarity : 0.005 0.049 2817 Dihedral : 13.724 175.526 3139 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.01 % Allowed : 19.40 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.19), residues: 1990 helix: 1.82 (0.18), residues: 844 sheet: -0.41 (0.27), residues: 345 loop : 0.14 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 43 TYR 0.014 0.001 TYR E 59 PHE 0.014 0.002 PHE E 521 TRP 0.011 0.001 TRP E 587 HIS 0.005 0.001 HIS F 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.21 (17129) covalent geometry : angle 0.58792 / 0.30 (23510) hydrogen bonds : bond 0.04465 / 3.14 ( 775) hydrogen bonds : angle 5.18707 / 3.85 ( 2203) metal coordination : bond 0.00372 / 0.21 ( 5) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8656 (tptt) REVERT: A 160 GLU cc_start: 0.8798 (pm20) cc_final: 0.8313 (pm20) REVERT: A 206 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8543 (tp) REVERT: B 64 ASP cc_start: 0.8760 (t0) cc_final: 0.8470 (t0) REVERT: B 143 GLN cc_start: 0.8807 (pm20) cc_final: 0.8603 (pm20) REVERT: B 160 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: C 64 ASP cc_start: 0.8910 (t0) cc_final: 0.8532 (t0) REVERT: C 229 ASP cc_start: 0.8666 (t70) cc_final: 0.8425 (t70) REVERT: D 64 ASP cc_start: 0.8820 (t0) cc_final: 0.8507 (t0) REVERT: D 179 THR cc_start: 0.9106 (t) cc_final: 0.8899 (m) REVERT: D 212 LYS cc_start: 0.8832 (tttt) cc_final: 0.7751 (tptt) REVERT: E 79 GLU cc_start: 0.8936 (tp30) cc_final: 0.8677 (tp30) REVERT: E 608 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9196 (ttpp) REVERT: E 713 MET cc_start: 0.8595 (mmm) cc_final: 0.8375 (mmm) REVERT: E 729 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: E 777 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8562 (tm-30) REVERT: E 780 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: F 161 LYS cc_start: 0.8834 (tmmm) cc_final: 0.8525 (ptmm) REVERT: F 162 ASN cc_start: 0.7147 (m-40) cc_final: 0.6668 (m-40) outliers start: 49 outliers final: 18 residues processed: 223 average time/residue: 0.5630 time to fit residues: 140.9115 Evaluate side-chains 191 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 126 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 112 optimal weight: 0.0020 chunk 132 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.3166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 ASN B 220 GLN F 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059932 restraints weight = 36111.635| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.04 r_work: 0.2838 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17135 Z= 0.117 Angle : 0.554 12.875 23510 Z= 0.279 Chirality : 0.041 0.158 2749 Planarity : 0.004 0.072 2817 Dihedral : 13.755 175.224 3139 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.64 % Allowed : 20.20 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 1990 helix: 1.90 (0.18), residues: 851 sheet: -0.36 (0.27), residues: 338 loop : 0.18 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.014 0.001 TYR E 59 PHE 0.013 0.001 PHE C 114 TRP 0.016 0.001 TRP E 587 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17129) covalent geometry : angle 0.55410 / 0.28 (23510) hydrogen bonds : bond 0.03811 / 2.71 ( 775) hydrogen bonds : angle 4.99827 / 3.71 ( 2203) metal coordination : bond 0.00276 / 0.15 ( 5) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8645 (tptt) REVERT: A 151 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 206 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8572 (tp) REVERT: A 259 MET cc_start: 0.9014 (mmm) cc_final: 0.8667 (mmm) REVERT: B 64 ASP cc_start: 0.8783 (t0) cc_final: 0.8500 (t0) REVERT: B 142 ASP cc_start: 0.8699 (p0) cc_final: 0.8493 (p0) REVERT: B 160 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: C 64 ASP cc_start: 0.8892 (t0) cc_final: 0.8569 (t0) REVERT: C 229 ASP cc_start: 0.8518 (t70) cc_final: 0.8295 (t70) REVERT: D 64 ASP cc_start: 0.8801 (t0) cc_final: 0.8480 (t0) REVERT: D 212 LYS cc_start: 0.8758 (tttt) cc_final: 0.7732 (tptt) REVERT: E 603 SER cc_start: 0.9150 (m) cc_final: 0.8944 (p) REVERT: E 608 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9176 (ttpp) REVERT: E 638 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8705 (mm-40) REVERT: E 729 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: F 217 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7508 (tpt90) outliers start: 43 outliers final: 9 residues processed: 224 average time/residue: 0.5039 time to fit residues: 126.3710 Evaluate side-chains 197 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 86 optimal weight: 0.2980 chunk 161 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 0.0470 chunk 140 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.078784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059196 restraints weight = 35930.972| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.03 r_work: 0.2821 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17135 Z= 0.153 Angle : 0.575 12.265 23510 Z= 0.287 Chirality : 0.041 0.152 2749 Planarity : 0.004 0.061 2817 Dihedral : 13.743 174.913 3139 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.01 % Allowed : 20.63 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 1990 helix: 1.94 (0.18), residues: 845 sheet: -0.43 (0.27), residues: 345 loop : 0.17 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 43 TYR 0.013 0.001 TYR E 59 PHE 0.013 0.001 PHE E 521 TRP 0.010 0.001 TRP E 587 HIS 0.003 0.001 HIS F 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (17129) covalent geometry : angle 0.57547 / 0.29 (23510) hydrogen bonds : bond 0.03806 / 2.70 ( 775) hydrogen bonds : angle 4.94955 / 3.67 ( 2203) metal coordination : bond 0.00278 / 0.17 ( 5) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8661 (tptt) REVERT: A 151 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 206 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8563 (tp) REVERT: B 64 ASP cc_start: 0.8791 (t0) cc_final: 0.8512 (t0) REVERT: B 160 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: C 64 ASP cc_start: 0.8914 (t0) cc_final: 0.8586 (t0) REVERT: C 229 ASP cc_start: 0.8554 (t70) cc_final: 0.8318 (t70) REVERT: D 64 ASP cc_start: 0.8836 (t0) cc_final: 0.8545 (t0) REVERT: D 212 LYS cc_start: 0.8753 (tttt) cc_final: 0.8101 (tttp) REVERT: E 608 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9159 (tppp) REVERT: E 713 MET cc_start: 0.8646 (mmm) cc_final: 0.8442 (mmm) REVERT: E 729 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: F 131 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8614 (ttpt) REVERT: F 217 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7528 (tpt90) outliers start: 49 outliers final: 17 residues processed: 224 average time/residue: 0.6025 time to fit residues: 150.6955 Evaluate side-chains 189 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 22 optimal weight: 0.7980 chunk 152 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 125 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN E 330 GLN E 638 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059288 restraints weight = 36152.236| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.03 r_work: 0.2825 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17135 Z= 0.143 Angle : 0.583 12.331 23510 Z= 0.291 Chirality : 0.041 0.153 2749 Planarity : 0.004 0.057 2817 Dihedral : 13.770 174.621 3139 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.58 % Allowed : 21.36 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1990 helix: 1.92 (0.18), residues: 850 sheet: -0.40 (0.27), residues: 338 loop : 0.10 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 43 TYR 0.013 0.001 TYR E 59 PHE 0.013 0.001 PHE E 521 TRP 0.012 0.001 TRP E 587 HIS 0.003 0.001 HIS E 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (17129) covalent geometry : angle 0.58303 / 0.29 (23510) hydrogen bonds : bond 0.03691 / 2.62 ( 775) hydrogen bonds : angle 4.91050 / 3.63 ( 2203) metal coordination : bond 0.00217 / 0.13 ( 5) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8610 (tptt) REVERT: A 151 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 206 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8514 (tp) REVERT: B 64 ASP cc_start: 0.8791 (t0) cc_final: 0.8483 (t0) REVERT: B 160 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: C 64 ASP cc_start: 0.8935 (t0) cc_final: 0.8568 (t0) REVERT: C 229 ASP cc_start: 0.8544 (t70) cc_final: 0.8305 (t70) REVERT: D 64 ASP cc_start: 0.8833 (t0) cc_final: 0.8509 (t0) REVERT: D 212 LYS cc_start: 0.8752 (tttt) cc_final: 0.7706 (tptt) REVERT: E 608 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9154 (tppp) REVERT: E 729 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: F 100 MET cc_start: 0.8660 (ppp) cc_final: 0.8392 (ppp) REVERT: F 131 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8563 (ttpt) REVERT: F 217 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7440 (tpt90) outliers start: 42 outliers final: 16 residues processed: 215 average time/residue: 0.5263 time to fit residues: 126.3175 Evaluate side-chains 195 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 194 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 152 optimal weight: 0.0010 chunk 134 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059317 restraints weight = 36592.876| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.06 r_work: 0.2824 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17135 Z= 0.145 Angle : 0.595 12.391 23510 Z= 0.296 Chirality : 0.041 0.153 2749 Planarity : 0.004 0.052 2817 Dihedral : 13.777 174.424 3139 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.33 % Allowed : 22.10 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1990 helix: 1.92 (0.18), residues: 850 sheet: -0.38 (0.27), residues: 338 loop : 0.09 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 43 TYR 0.012 0.001 TYR E 59 PHE 0.013 0.001 PHE E 521 TRP 0.013 0.001 TRP E 587 HIS 0.002 0.001 HIS F 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (17129) covalent geometry : angle 0.59535 / 0.30 (23510) hydrogen bonds : bond 0.03611 / 2.56 ( 775) hydrogen bonds : angle 4.87769 / 3.61 ( 2203) metal coordination : bond 0.00215 / 0.13 ( 5) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8629 (tptt) REVERT: A 151 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 206 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8511 (tp) REVERT: B 64 ASP cc_start: 0.8782 (t0) cc_final: 0.8499 (t0) REVERT: B 116 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.8208 (ttp-170) REVERT: B 160 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: C 64 ASP cc_start: 0.8946 (t0) cc_final: 0.8722 (t0) REVERT: C 229 ASP cc_start: 0.8535 (t70) cc_final: 0.8309 (t70) REVERT: C 232 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8351 (mt-10) REVERT: D 64 ASP cc_start: 0.8844 (t0) cc_final: 0.8502 (t0) REVERT: D 212 LYS cc_start: 0.8751 (tttt) cc_final: 0.7776 (tptt) REVERT: E 608 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9157 (tppp) REVERT: E 729 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8609 (m-80) REVERT: F 217 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7454 (tpt90) outliers start: 38 outliers final: 16 residues processed: 210 average time/residue: 0.5231 time to fit residues: 123.1112 Evaluate side-chains 196 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 195 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 201 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 170 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN B 220 GLN E 96 GLN E 638 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058968 restraints weight = 36550.634| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.04 r_work: 0.2817 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17135 Z= 0.163 Angle : 0.607 12.596 23510 Z= 0.301 Chirality : 0.042 0.164 2749 Planarity : 0.004 0.057 2817 Dihedral : 13.795 174.221 3139 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.90 % Allowed : 22.53 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1990 helix: 1.91 (0.18), residues: 850 sheet: -0.43 (0.27), residues: 345 loop : 0.10 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 43 TYR 0.012 0.001 TYR E 59 PHE 0.013 0.001 PHE E 521 TRP 0.011 0.001 TRP E 587 HIS 0.005 0.001 HIS E 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (17129) covalent geometry : angle 0.60696 / 0.30 (23510) hydrogen bonds : bond 0.03663 / 2.59 ( 775) hydrogen bonds : angle 4.87920 / 3.61 ( 2203) metal coordination : bond 0.00256 / 0.15 ( 5) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8450 (mp) REVERT: A 206 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8493 (tp) REVERT: B 64 ASP cc_start: 0.8775 (t0) cc_final: 0.8480 (t0) REVERT: B 116 ARG cc_start: 0.8501 (ttp-110) cc_final: 0.8214 (ttp-170) REVERT: B 160 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: C 64 ASP cc_start: 0.8934 (t0) cc_final: 0.8685 (t0) REVERT: C 229 ASP cc_start: 0.8557 (t70) cc_final: 0.8327 (t70) REVERT: C 232 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8348 (mt-10) REVERT: D 64 ASP cc_start: 0.8844 (t0) cc_final: 0.8494 (t0) REVERT: D 212 LYS cc_start: 0.8768 (tttt) cc_final: 0.7795 (tptt) REVERT: E 608 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9168 (ttpp) REVERT: E 654 VAL cc_start: 0.8938 (t) cc_final: 0.8653 (p) REVERT: F 217 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7443 (tpt90) outliers start: 31 outliers final: 16 residues processed: 203 average time/residue: 0.5721 time to fit residues: 130.3544 Evaluate side-chains 193 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 171 optimal weight: 10.0000 chunk 136 optimal weight: 0.5980 chunk 131 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058755 restraints weight = 36399.878| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.03 r_work: 0.2813 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17135 Z= 0.173 Angle : 0.616 13.272 23510 Z= 0.306 Chirality : 0.042 0.155 2749 Planarity : 0.004 0.056 2817 Dihedral : 13.821 174.025 3139 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.90 % Allowed : 22.53 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 1990 helix: 1.85 (0.18), residues: 850 sheet: -0.44 (0.27), residues: 345 loop : 0.11 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 43 TYR 0.016 0.001 TYR E 729 PHE 0.013 0.001 PHE E 521 TRP 0.009 0.001 TRP E 587 HIS 0.003 0.001 HIS F 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 (17129) covalent geometry : angle 0.61590 / 0.31 (23510) hydrogen bonds : bond 0.03718 / 2.62 ( 775) hydrogen bonds : angle 4.89195 / 3.61 ( 2203) metal coordination : bond 0.00301 / 0.18 ( 5) Misc. bond : bond 0.00012 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 206 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8479 (tp) REVERT: B 64 ASP cc_start: 0.8777 (t0) cc_final: 0.8483 (t0) REVERT: B 116 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.8197 (ttp-170) REVERT: B 160 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: C 64 ASP cc_start: 0.8963 (t0) cc_final: 0.8712 (t0) REVERT: C 229 ASP cc_start: 0.8560 (t70) cc_final: 0.8328 (t70) REVERT: C 232 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8384 (mt-10) REVERT: D 64 ASP cc_start: 0.8844 (t0) cc_final: 0.8519 (t0) REVERT: D 212 LYS cc_start: 0.8763 (tttt) cc_final: 0.7781 (tptt) REVERT: E 608 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9171 (ttpp) REVERT: E 654 VAL cc_start: 0.8947 (t) cc_final: 0.8668 (p) REVERT: F 217 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7453 (tpt90) outliers start: 31 outliers final: 17 residues processed: 200 average time/residue: 0.6142 time to fit residues: 137.4096 Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 113 optimal weight: 0.0980 chunk 124 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 194 optimal weight: 0.0570 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN C 143 GLN ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.059531 restraints weight = 36152.768| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.04 r_work: 0.2831 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17135 Z= 0.132 Angle : 0.607 13.199 23510 Z= 0.300 Chirality : 0.041 0.151 2749 Planarity : 0.004 0.049 2817 Dihedral : 13.817 174.224 3139 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.78 % Allowed : 22.59 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 1990 helix: 1.91 (0.18), residues: 851 sheet: -0.43 (0.27), residues: 343 loop : 0.11 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 43 TYR 0.012 0.001 TYR E 59 PHE 0.012 0.001 PHE E 521 TRP 0.011 0.001 TRP E 587 HIS 0.002 0.001 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (17129) covalent geometry : angle 0.60725 / 0.30 (23510) hydrogen bonds : bond 0.03478 / 2.46 ( 775) hydrogen bonds : angle 4.83442 / 3.58 ( 2203) metal coordination : bond 0.00185 / 0.10 ( 5) Misc. bond : bond 0.00020 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5181.72 seconds wall clock time: 89 minutes 17.36 seconds (5357.36 seconds total)