Starting phenix.real_space_refine on Sun Aug 24 03:16:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey0_50050/08_2025/9ey0_50050.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey0_50050/08_2025/9ey0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ey0_50050/08_2025/9ey0_50050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey0_50050/08_2025/9ey0_50050.map" model { file = "/net/cci-nas-00/data/ceres_data/9ey0_50050/08_2025/9ey0_50050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey0_50050/08_2025/9ey0_50050.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 4.34, per 1000 atoms: 0.26 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: 1.63 Conformation dependent library (CDL) restraints added in 704.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.34 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: 3.41 Time building geometry restraints manager: 2.08 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: 23286 2.66 - 5.31: 196 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: 2460 0.065 - 0.130: 275 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: 5.160 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.140 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 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= 0.272 Angle : 0.559 13.287 23510 Z= 0.305 Chirality : 0.041 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 aren 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 covalent geometry : bond 0.00454 (17129) covalent geometry : angle 0.55857 (23510) hydrogen bonds : bond 0.22334 ( 775) hydrogen bonds : angle 8.07919 ( 2203) metal coordination : bond 0.26388 ( 5) Misc. bond : bond 0.00061 ( 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 : 0.717 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: 0.6734 time to fit residues: 142.8680 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 : 0.648 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 220 GLN D 102 ASN E 355 GLN E 393 HIS ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059612 restraints weight = 35635.116| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.02 r_work: 0.2831 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17135 Z= 0.159 Angle : 0.573 7.426 23510 Z= 0.287 Chirality : 0.042 0.168 2749 Planarity : 0.004 0.042 2817 Dihedral : 13.666 179.313 3139 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.76 % Allowed : 17.00 % Favored : 80.23 % 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 aren not related in a simple way. whole: 1.52 (0.20), residues: 1990 helix: 2.18 (0.18), residues: 844 sheet: -0.12 (0.29), residues: 340 loop : 0.38 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 43 TYR 0.013 0.001 TYR E 59 PHE 0.014 0.001 PHE E 521 TRP 0.012 0.001 TRP E 587 HIS 0.004 0.001 HIS E 647 Details of bonding type rmsd covalent geometry : bond 0.00381 (17129) covalent geometry : angle 0.57250 (23510) hydrogen bonds : bond 0.04365 ( 775) hydrogen bonds : angle 5.38900 ( 2203) metal coordination : bond 0.00686 ( 5) Misc. bond : bond 0.00011 ( 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 251 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ARG cc_start: 0.8664 (ppt170) cc_final: 0.8202 (ppt170) REVERT: C 64 ASP cc_start: 0.8874 (t0) cc_final: 0.8583 (t0) REVERT: C 70 ASP cc_start: 0.8610 (m-30) cc_final: 0.8404 (m-30) REVERT: D 179 THR cc_start: 0.9164 (t) cc_final: 0.8902 (m) REVERT: D 211 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7831 (tm-30) REVERT: E 38 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7498 (mtp85) REVERT: E 60 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8440 (tm) REVERT: E 608 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9167 (tppp) REVERT: E 713 MET cc_start: 0.8652 (mmm) cc_final: 0.8412 (mmm) outliers start: 45 outliers final: 11 residues processed: 235 average time/residue: 0.6353 time to fit residues: 165.9061 Evaluate side-chains 180 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 629 LEU 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: 0.6980 chunk 115 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 355 GLN ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.078558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058688 restraints weight = 36625.709| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.05 r_work: 0.2809 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1843 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= 0.166 Angle : 0.558 8.341 23510 Z= 0.278 Chirality : 0.042 0.158 2749 Planarity : 0.004 0.041 2817 Dihedral : 13.761 174.828 3139 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.07 % Allowed : 18.23 % 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 aren not related in a simple way. whole: 1.37 (0.19), residues: 1990 helix: 2.08 (0.18), residues: 845 sheet: -0.27 (0.28), residues: 345 loop : 0.31 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.013 0.001 TYR E 59 PHE 0.012 0.001 PHE E 521 TRP 0.010 0.001 TRP E 587 HIS 0.004 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00400 (17129) covalent geometry : angle 0.55800 (23510) hydrogen bonds : bond 0.03945 ( 775) hydrogen bonds : angle 5.07930 ( 2203) metal coordination : bond 0.00331 ( 5) Misc. bond : bond 0.00017 ( 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 255 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8638 (tptt) REVERT: A 151 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 206 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8541 (tp) REVERT: B 64 ASP cc_start: 0.8737 (t0) cc_final: 0.8494 (t0) REVERT: B 160 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: B 226 ARG cc_start: 0.8663 (ppt170) cc_final: 0.8119 (ppt170) REVERT: C 64 ASP cc_start: 0.8898 (t0) cc_final: 0.8639 (t0) REVERT: C 70 ASP cc_start: 0.8561 (m-30) cc_final: 0.8343 (m-30) REVERT: C 140 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: D 160 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: D 212 LYS cc_start: 0.8744 (tttt) cc_final: 0.8086 (tttp) REVERT: E 60 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8410 (tm) REVERT: E 79 GLU cc_start: 0.8953 (tp30) cc_final: 0.8671 (tp30) REVERT: E 262 MET cc_start: 0.8088 (tmm) cc_final: 0.7782 (ttp) REVERT: E 461 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8631 (tm-30) REVERT: E 603 SER cc_start: 0.9136 (m) cc_final: 0.8926 (p) REVERT: E 608 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9162 (tppp) REVERT: E 638 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8706 (mm-40) REVERT: E 776 GLU cc_start: 0.9055 (pp20) cc_final: 0.8757 (pp20) REVERT: E 780 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8403 (mp0) outliers start: 50 outliers final: 13 residues processed: 242 average time/residue: 0.6798 time to fit residues: 182.0142 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 : 0.570 ------------------------------------------------------------------------------- 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 B residue 214 CYS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 617 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 128 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 86 ASN E 330 GLN ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057975 restraints weight = 36469.074| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.04 r_work: 0.2792 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17135 Z= 0.196 Angle : 0.591 8.597 23510 Z= 0.292 Chirality : 0.042 0.158 2749 Planarity : 0.004 0.045 2817 Dihedral : 13.854 172.366 3139 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.74 % Allowed : 18.72 % Favored : 77.53 % 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 aren not related in a simple way. whole: 1.19 (0.19), residues: 1990 helix: 1.93 (0.18), residues: 846 sheet: -0.39 (0.27), residues: 345 loop : 0.22 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 166 TYR 0.012 0.001 TYR E 59 PHE 0.013 0.001 PHE E 521 TRP 0.009 0.001 TRP E 587 HIS 0.004 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00478 (17129) covalent geometry : angle 0.59143 (23510) hydrogen bonds : bond 0.03868 ( 775) hydrogen bonds : angle 5.00919 ( 2203) metal coordination : bond 0.00354 ( 5) Misc. bond : bond 0.00010 ( 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 257 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8656 (tptt) REVERT: A 151 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8470 (mp) REVERT: A 206 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8484 (tp) REVERT: B 64 ASP cc_start: 0.8781 (t0) cc_final: 0.8510 (t0) REVERT: B 160 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: B 251 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8897 (mm) REVERT: C 64 ASP cc_start: 0.8896 (t0) cc_final: 0.8608 (t0) REVERT: C 70 ASP cc_start: 0.8565 (m-30) cc_final: 0.8351 (m-30) REVERT: C 229 ASP cc_start: 0.8629 (t0) cc_final: 0.8350 (t0) REVERT: D 52 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8620 (tptp) REVERT: D 212 LYS cc_start: 0.8764 (tttt) cc_final: 0.8127 (tttp) REVERT: E 38 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7423 (mtp85) REVERT: E 60 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8434 (tm) REVERT: E 162 GLU cc_start: 0.8116 (tp30) cc_final: 0.7755 (tp30) REVERT: E 262 MET cc_start: 0.8125 (tmm) cc_final: 0.7732 (ttp) REVERT: E 461 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8664 (tm-30) REVERT: E 603 SER cc_start: 0.9157 (m) cc_final: 0.8884 (p) REVERT: E 608 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9176 (tppp) REVERT: E 695 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8734 (mp0) REVERT: E 713 MET cc_start: 0.8692 (mmm) cc_final: 0.8456 (mmm) REVERT: E 776 GLU cc_start: 0.9108 (pp20) cc_final: 0.8824 (pp20) REVERT: E 780 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: E 785 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8617 (ttp80) REVERT: F 217 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7491 (tpt90) outliers start: 61 outliers final: 20 residues processed: 241 average time/residue: 0.6721 time to fit residues: 179.6457 Evaluate side-chains 196 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 132 VAL 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 A residue 217 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 B residue 251 ILE 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 60 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 511 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 695 GLU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 785 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 126 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 112 optimal weight: 0.1980 chunk 132 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 220 GLN C 143 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 527 HIS E 638 GLN F 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059487 restraints weight = 36408.827| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.05 r_work: 0.2827 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17135 Z= 0.126 Angle : 0.555 9.692 23510 Z= 0.272 Chirality : 0.041 0.147 2749 Planarity : 0.004 0.045 2817 Dihedral : 13.808 172.591 3139 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.44 % Allowed : 19.52 % Favored : 77.04 % 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 aren not related in a simple way. whole: 1.25 (0.19), residues: 1990 helix: 2.05 (0.18), residues: 851 sheet: -0.36 (0.27), residues: 343 loop : 0.16 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.012 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 covalent geometry : bond 0.00303 (17129) covalent geometry : angle 0.55490 (23510) hydrogen bonds : bond 0.03273 ( 775) hydrogen bonds : angle 4.83441 ( 2203) metal coordination : bond 0.00214 ( 5) Misc. bond : bond 0.00020 ( 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 259 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8581 (tptt) REVERT: A 206 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8489 (tp) REVERT: B 64 ASP cc_start: 0.8782 (t0) cc_final: 0.8493 (t0) REVERT: B 100 THR cc_start: 0.8873 (m) cc_final: 0.8514 (t) REVERT: B 160 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: B 226 ARG cc_start: 0.8697 (ppt170) cc_final: 0.8309 (ppt170) REVERT: C 64 ASP cc_start: 0.8839 (t0) cc_final: 0.8610 (t0) REVERT: C 70 ASP cc_start: 0.8575 (m-30) cc_final: 0.8321 (m-30) REVERT: C 229 ASP cc_start: 0.8536 (t0) cc_final: 0.8274 (t0) REVERT: D 52 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8641 (tptp) REVERT: D 212 LYS cc_start: 0.8775 (tttt) cc_final: 0.8010 (pptt) REVERT: E 60 LEU cc_start: 0.8696 (tp) cc_final: 0.8406 (tm) REVERT: E 147 TYR cc_start: 0.8738 (t80) cc_final: 0.8516 (t80) REVERT: E 163 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8483 (mm) REVERT: E 262 MET cc_start: 0.8075 (tmm) cc_final: 0.7707 (ttp) REVERT: E 461 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8731 (tm-30) REVERT: E 638 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8666 (mm-40) REVERT: E 713 MET cc_start: 0.8672 (mmm) cc_final: 0.8404 (mmm) REVERT: E 776 GLU cc_start: 0.9120 (pp20) cc_final: 0.8858 (pp20) REVERT: E 780 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: F 217 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7406 (tpt90) outliers start: 56 outliers final: 14 residues processed: 245 average time/residue: 0.6249 time to fit residues: 169.9221 Evaluate side-chains 204 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 143 GLN 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 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 511 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 638 GLN Chi-restraints excluded: chain E residue 780 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 86 optimal weight: 0.3980 chunk 161 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 167 optimal weight: 0.2980 chunk 169 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 220 GLN D 260 GLN E 96 GLN E 355 GLN ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.078854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059122 restraints weight = 36209.808| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.03 r_work: 0.2821 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2258 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= 0.146 Angle : 0.570 10.250 23510 Z= 0.281 Chirality : 0.041 0.153 2749 Planarity : 0.004 0.046 2817 Dihedral : 13.804 172.296 3139 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.19 % Allowed : 20.56 % Favored : 76.24 % 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 aren not related in a simple way. whole: 1.25 (0.19), residues: 1990 helix: 2.01 (0.18), residues: 853 sheet: -0.30 (0.27), residues: 358 loop : 0.16 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 43 TYR 0.012 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 E 39 Details of bonding type rmsd covalent geometry : bond 0.00354 (17129) covalent geometry : angle 0.57043 (23510) hydrogen bonds : bond 0.03363 ( 775) hydrogen bonds : angle 4.80337 ( 2203) metal coordination : bond 0.00252 ( 5) Misc. bond : bond 0.00015 ( 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 242 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8519 (tptt) REVERT: A 151 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 206 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8468 (tp) REVERT: B 64 ASP cc_start: 0.8768 (t0) cc_final: 0.8486 (t0) REVERT: B 160 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: B 226 ARG cc_start: 0.8695 (ppt170) cc_final: 0.8268 (ppt170) REVERT: C 64 ASP cc_start: 0.8830 (t0) cc_final: 0.8596 (t0) REVERT: C 70 ASP cc_start: 0.8552 (m-30) cc_final: 0.8345 (m-30) REVERT: C 229 ASP cc_start: 0.8511 (t0) cc_final: 0.8294 (t0) REVERT: D 52 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8656 (tptp) REVERT: D 212 LYS cc_start: 0.8747 (tttt) cc_final: 0.8007 (pptt) REVERT: E 38 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7434 (mtp85) REVERT: E 60 LEU cc_start: 0.8698 (tp) cc_final: 0.8390 (tm) REVERT: E 162 GLU cc_start: 0.8098 (tp30) cc_final: 0.7809 (tp30) REVERT: E 163 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8573 (mm) REVERT: E 262 MET cc_start: 0.8134 (tmm) cc_final: 0.7792 (ttp) REVERT: E 412 LEU cc_start: 0.8001 (pt) cc_final: 0.7407 (mp) REVERT: E 457 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8464 (tm-30) REVERT: E 608 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9172 (ttpp) REVERT: E 776 GLU cc_start: 0.9101 (pp20) cc_final: 0.8832 (pp20) REVERT: E 780 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: F 217 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7381 (tpt90) outliers start: 52 outliers final: 15 residues processed: 231 average time/residue: 0.6103 time to fit residues: 157.3902 Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE 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 B residue 259 MET 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 511 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 285 ASP 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: 1.9990 chunk 152 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 86 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 125 optimal weight: 0.0570 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 143 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3373 r_free = 0.3373 target = 0.079988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.060593 restraints weight = 35986.941| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.04 r_work: 0.2854 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2373 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= 0.113 Angle : 0.565 10.876 23510 Z= 0.275 Chirality : 0.041 0.142 2749 Planarity : 0.004 0.046 2817 Dihedral : 13.754 172.647 3139 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.46 % Allowed : 21.49 % 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 aren not related in a simple way. whole: 1.33 (0.19), residues: 1990 helix: 2.11 (0.18), residues: 850 sheet: -0.26 (0.27), residues: 353 loop : 0.17 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 785 TYR 0.012 0.001 TYR E 59 PHE 0.012 0.001 PHE E 521 TRP 0.010 0.001 TRP E 587 HIS 0.002 0.000 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00269 (17129) covalent geometry : angle 0.56484 (23510) hydrogen bonds : bond 0.03007 ( 775) hydrogen bonds : angle 4.66931 ( 2203) metal coordination : bond 0.00169 ( 5) Misc. bond : bond 0.00020 ( 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 239 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8576 (tptt) REVERT: A 151 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 206 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8520 (tp) REVERT: A 259 MET cc_start: 0.8714 (mmm) cc_final: 0.8270 (mmm) REVERT: B 64 ASP cc_start: 0.8740 (t0) cc_final: 0.8477 (t0) REVERT: B 100 THR cc_start: 0.8844 (m) cc_final: 0.8540 (t) REVERT: B 160 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: B 226 ARG cc_start: 0.8714 (ppt170) cc_final: 0.8329 (ppt170) REVERT: C 64 ASP cc_start: 0.8821 (t0) cc_final: 0.8593 (t0) REVERT: C 70 ASP cc_start: 0.8520 (m-30) cc_final: 0.8304 (m-30) REVERT: C 229 ASP cc_start: 0.8483 (t0) cc_final: 0.8268 (t0) REVERT: D 48 GLU cc_start: 0.8163 (pm20) cc_final: 0.7897 (pm20) REVERT: D 52 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8694 (tptp) REVERT: D 212 LYS cc_start: 0.8727 (tttt) cc_final: 0.8016 (pptt) REVERT: E 38 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7330 (mtp85) REVERT: E 163 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8584 (mm) REVERT: E 457 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8394 (tm-30) REVERT: E 713 MET cc_start: 0.8782 (mmm) cc_final: 0.8484 (mmm) REVERT: E 776 GLU cc_start: 0.9065 (pp20) cc_final: 0.8757 (pp20) REVERT: E 780 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: F 100 MET cc_start: 0.8712 (ppp) cc_final: 0.8466 (ppp) REVERT: F 217 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7382 (tpt90) outliers start: 40 outliers final: 11 residues processed: 228 average time/residue: 0.5555 time to fit residues: 141.0947 Evaluate side-chains 200 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 259 MET 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 163 LEU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 285 ASP 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: 7.9990 chunk 62 optimal weight: 0.7980 chunk 152 optimal weight: 0.0870 chunk 134 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 191 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3350 r_free = 0.3350 target = 0.078733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059254 restraints weight = 36408.172| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.05 r_work: 0.2823 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2409 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= 0.155 Angle : 0.598 10.259 23510 Z= 0.292 Chirality : 0.041 0.148 2749 Planarity : 0.004 0.047 2817 Dihedral : 13.799 175.467 3139 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.39 % Allowed : 22.59 % Favored : 75.02 % 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 aren not related in a simple way. whole: 1.26 (0.19), residues: 1990 helix: 2.07 (0.18), residues: 847 sheet: -0.30 (0.27), residues: 358 loop : 0.12 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 43 TYR 0.012 0.001 TYR E 59 PHE 0.013 0.001 PHE E 771 TRP 0.018 0.001 TRP E 587 HIS 0.003 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00377 (17129) covalent geometry : angle 0.59807 (23510) hydrogen bonds : bond 0.03350 ( 775) hydrogen bonds : angle 4.72716 ( 2203) metal coordination : bond 0.00281 ( 5) Misc. bond : bond 0.00015 ( 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 221 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8570 (tptt) REVERT: A 151 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 206 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8506 (tp) REVERT: B 64 ASP cc_start: 0.8761 (t0) cc_final: 0.8487 (t0) REVERT: B 69 LYS cc_start: 0.8807 (tmmm) cc_final: 0.8605 (tmmm) REVERT: B 160 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: B 226 ARG cc_start: 0.8695 (ppt170) cc_final: 0.8277 (ppt170) REVERT: C 64 ASP cc_start: 0.8809 (t0) cc_final: 0.8592 (t0) REVERT: C 70 ASP cc_start: 0.8541 (m-30) cc_final: 0.8340 (m-30) REVERT: C 229 ASP cc_start: 0.8518 (t0) cc_final: 0.8305 (t0) REVERT: D 48 GLU cc_start: 0.8134 (pm20) cc_final: 0.7910 (pm20) REVERT: D 52 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8712 (tptp) REVERT: D 212 LYS cc_start: 0.8717 (tttt) cc_final: 0.8014 (pptt) REVERT: E 38 ARG cc_start: 0.7638 (mtp85) cc_final: 0.7299 (mtp85) REVERT: E 457 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8428 (tm-30) REVERT: E 608 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9173 (ttpp) REVERT: E 647 HIS cc_start: 0.7905 (m90) cc_final: 0.7523 (m90) REVERT: E 654 VAL cc_start: 0.8972 (t) cc_final: 0.8706 (p) REVERT: E 713 MET cc_start: 0.8756 (mmm) cc_final: 0.8485 (mmm) REVERT: E 776 GLU cc_start: 0.9104 (pp20) cc_final: 0.8844 (pp20) REVERT: E 780 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: F 100 MET cc_start: 0.8772 (ppp) cc_final: 0.8513 (ppp) REVERT: F 217 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7431 (tpt90) outliers start: 39 outliers final: 16 residues processed: 213 average time/residue: 0.6310 time to fit residues: 149.3810 Evaluate side-chains 201 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE 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 B residue 259 MET 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 D residue 237 VAL Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 780 GLU 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 285 ASP 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: 0.2980 chunk 48 optimal weight: 0.5980 chunk 201 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 148 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 143 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.079364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.059921 restraints weight = 36092.936| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.03 r_work: 0.2841 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17135 Z= 0.136 Angle : 0.600 13.324 23510 Z= 0.292 Chirality : 0.041 0.152 2749 Planarity : 0.004 0.087 2817 Dihedral : 13.805 179.839 3139 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.27 % Allowed : 22.77 % Favored : 74.95 % 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 aren not related in a simple way. whole: 1.25 (0.19), residues: 1990 helix: 2.07 (0.18), residues: 847 sheet: -0.31 (0.27), residues: 358 loop : 0.12 (0.23), residues: 785 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 0.013 0.001 PHE E 521 TRP 0.010 0.001 TRP E 587 HIS 0.002 0.001 HIS E 342 Details of bonding type rmsd covalent geometry : bond 0.00331 (17129) covalent geometry : angle 0.60014 (23510) hydrogen bonds : bond 0.03197 ( 775) hydrogen bonds : angle 4.70478 ( 2203) metal coordination : bond 0.00231 ( 5) Misc. bond : bond 0.00019 ( 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 229 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8556 (tptt) REVERT: A 151 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8529 (mp) REVERT: B 64 ASP cc_start: 0.8738 (t0) cc_final: 0.8452 (t0) REVERT: B 100 THR cc_start: 0.8844 (m) cc_final: 0.8493 (t) REVERT: B 160 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: B 226 ARG cc_start: 0.8712 (ppt170) cc_final: 0.8309 (ppt170) REVERT: C 64 ASP cc_start: 0.8828 (t0) cc_final: 0.8613 (t0) REVERT: C 70 ASP cc_start: 0.8598 (m-30) cc_final: 0.8362 (m-30) REVERT: C 229 ASP cc_start: 0.8491 (t0) cc_final: 0.8275 (t0) REVERT: D 52 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8740 (tptp) REVERT: D 212 LYS cc_start: 0.8718 (tttt) cc_final: 0.7998 (pptt) REVERT: E 38 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7265 (mtp85) REVERT: E 461 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8783 (tm-30) REVERT: E 608 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9177 (ttpp) REVERT: E 647 HIS cc_start: 0.7920 (m90) cc_final: 0.7508 (m90) REVERT: E 654 VAL cc_start: 0.8945 (t) cc_final: 0.8678 (p) REVERT: E 713 MET cc_start: 0.8779 (mmm) cc_final: 0.8525 (mmm) REVERT: E 776 GLU cc_start: 0.9118 (pp20) cc_final: 0.8785 (pp20) REVERT: E 780 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: F 100 MET cc_start: 0.8782 (ppp) cc_final: 0.8537 (ppp) REVERT: F 217 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7434 (tpt90) outliers start: 37 outliers final: 18 residues processed: 219 average time/residue: 0.6801 time to fit residues: 165.2685 Evaluate side-chains 205 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE 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 B residue 259 MET 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 438 ILE Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 285 ASP 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: 3.9990 chunk 136 optimal weight: 0.9980 chunk 131 optimal weight: 0.0370 chunk 160 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3322 r_free = 0.3322 target = 0.077179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057612 restraints weight = 36080.615| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.02 r_work: 0.2786 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17135 Z= 0.242 Angle : 0.667 13.239 23510 Z= 0.328 Chirality : 0.044 0.159 2749 Planarity : 0.005 0.087 2817 Dihedral : 13.888 173.208 3139 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.90 % Allowed : 23.08 % Favored : 75.02 % 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 aren not related in a simple way. whole: 1.04 (0.19), residues: 1990 helix: 1.84 (0.18), residues: 843 sheet: -0.41 (0.27), residues: 360 loop : 0.09 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 43 TYR 0.011 0.001 TYR E 59 PHE 0.014 0.002 PHE C 223 TRP 0.009 0.001 TRP E 659 HIS 0.004 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00595 (17129) covalent geometry : angle 0.66655 (23510) hydrogen bonds : bond 0.03959 ( 775) hydrogen bonds : angle 4.94037 ( 2203) metal coordination : bond 0.00453 ( 5) Misc. bond : bond 0.00010 ( 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 204 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8528 (mp) REVERT: B 64 ASP cc_start: 0.8792 (t0) cc_final: 0.8494 (t0) REVERT: B 160 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: C 64 ASP cc_start: 0.8945 (t0) cc_final: 0.8696 (t0) REVERT: C 70 ASP cc_start: 0.8631 (m-30) cc_final: 0.8427 (m-30) REVERT: C 229 ASP cc_start: 0.8555 (t0) cc_final: 0.8337 (t0) REVERT: D 52 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8683 (tptp) REVERT: D 212 LYS cc_start: 0.8703 (tttt) cc_final: 0.8136 (pptt) REVERT: E 38 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7366 (mtp85) REVERT: E 60 LEU cc_start: 0.8764 (tp) cc_final: 0.8471 (tm) REVERT: E 178 MET cc_start: 0.9022 (ptt) cc_final: 0.8740 (ptt) REVERT: E 461 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8693 (tm-30) REVERT: E 608 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9192 (ttpp) REVERT: E 654 VAL cc_start: 0.8972 (t) cc_final: 0.8697 (p) REVERT: E 713 MET cc_start: 0.8726 (mmm) cc_final: 0.8489 (mmm) REVERT: E 776 GLU cc_start: 0.9150 (pp20) cc_final: 0.8859 (pp20) REVERT: E 780 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: F 100 MET cc_start: 0.8805 (ppp) cc_final: 0.8577 (ppp) REVERT: F 217 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7480 (tpt90) outliers start: 31 outliers final: 17 residues processed: 193 average time/residue: 0.6576 time to fit residues: 141.4918 Evaluate side-chains 190 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 160 GLU 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 D residue 237 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 285 ASP 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: 0.8980 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 201 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 142 optimal weight: 0.3980 chunk 194 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 143 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3350 r_free = 0.3350 target = 0.078548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059120 restraints weight = 35689.209| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.01 r_work: 0.2823 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17135 Z= 0.156 Angle : 0.630 13.194 23510 Z= 0.307 Chirality : 0.042 0.184 2749 Planarity : 0.004 0.080 2817 Dihedral : 13.855 173.276 3139 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.84 % Allowed : 23.45 % Favored : 74.71 % 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 aren not related in a simple way. whole: 1.07 (0.19), residues: 1990 helix: 1.91 (0.18), residues: 848 sheet: -0.41 (0.27), residues: 358 loop : 0.05 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 43 TYR 0.011 0.001 TYR E 59 PHE 0.014 0.001 PHE E 521 TRP 0.011 0.001 TRP E 587 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00381 (17129) covalent geometry : angle 0.62992 (23510) hydrogen bonds : bond 0.03405 ( 775) hydrogen bonds : angle 4.81027 ( 2203) metal coordination : bond 0.00287 ( 5) Misc. bond : bond 0.00017 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6075.07 seconds wall clock time: 104 minutes 31.01 seconds (6271.01 seconds total)