Starting phenix.real_space_refine on Tue Jan 21 09:06:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey0_50050/01_2025/9ey0_50050.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey0_50050/01_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_50050/01_2025/9ey0_50050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey0_50050/01_2025/9ey0_50050.map" model { file = "/net/cci-nas-00/data/ceres_data/9ey0_50050/01_2025/9ey0_50050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey0_50050/01_2025/9ey0_50050.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 11.02, per 1000 atoms: 0.66 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: 4.51 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 6.45 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: 6.72 Time building geometry restraints manager: 5.15 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: 4.010 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 48.320 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.760 ------------------------------------------------------------------------------- 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 : 0.005 0.286 17129 Z= 0.327 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.004 0.001 TRP E 659 HIS 0.002 0.000 HIS E 546 PHE 0.007 0.001 PHE F 312 TYR 0.008 0.001 TYR D 101 ARG 0.003 0.000 ARG E 430 *********************** 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 : 1.886 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: 1.3871 time to fit residues: 295.4043 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 : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 159 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 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 102 ASN B 220 GLN D 102 ASN E 393 HIS ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059732 restraints weight = 35952.087| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.02 r_work: 0.2833 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17129 Z= 0.237 Angle : 0.570 7.518 23510 Z= 0.285 Chirality : 0.042 0.180 2749 Planarity : 0.004 0.043 2817 Dihedral : 13.661 179.361 3139 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.70 % Allowed : 17.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1990 helix: 2.19 (0.18), residues: 844 sheet: -0.11 (0.29), residues: 340 loop : 0.38 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 587 HIS 0.004 0.001 HIS E 342 PHE 0.013 0.001 PHE F 97 TYR 0.013 0.001 TYR E 59 ARG 0.011 0.000 ARG E 43 *********************** 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: 44 poor density : 207 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ARG cc_start: 0.8665 (ppt170) cc_final: 0.8206 (ppt170) REVERT: C 64 ASP cc_start: 0.8870 (t0) cc_final: 0.8583 (t0) REVERT: C 70 ASP cc_start: 0.8607 (m-30) cc_final: 0.8403 (m-30) REVERT: D 179 THR cc_start: 0.9164 (t) cc_final: 0.8899 (m) REVERT: D 211 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7805 (tm-30) REVERT: E 38 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7502 (mtp85) REVERT: E 60 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8432 (tm) REVERT: E 608 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9167 (tppp) outliers start: 44 outliers final: 11 residues processed: 238 average time/residue: 1.3871 time to fit residues: 366.6788 Evaluate side-chains 178 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 1.916 ------------------------------------------------------------------------------- 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 183 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 170 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.079433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059617 restraints weight = 36157.065| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.04 r_work: 0.2832 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17129 Z= 0.212 Angle : 0.543 8.648 23510 Z= 0.269 Chirality : 0.041 0.148 2749 Planarity : 0.004 0.040 2817 Dihedral : 13.705 175.242 3139 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.70 % Allowed : 18.48 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 1990 helix: 2.14 (0.18), residues: 849 sheet: -0.21 (0.28), residues: 343 loop : 0.29 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 587 HIS 0.003 0.001 HIS E 647 PHE 0.011 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.007 0.000 ARG E 46 *********************** 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 258 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8620 (tptt) REVERT: B 64 ASP cc_start: 0.8716 (t0) cc_final: 0.8478 (t0) REVERT: B 160 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: B 226 ARG cc_start: 0.8639 (ppt170) cc_final: 0.8334 (ppt170) REVERT: C 64 ASP cc_start: 0.8869 (t0) cc_final: 0.8500 (t0) REVERT: C 70 ASP cc_start: 0.8546 (m-30) cc_final: 0.8334 (m-30) REVERT: C 140 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: D 48 GLU cc_start: 0.8168 (pm20) cc_final: 0.7967 (pm20) REVERT: D 160 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: E 60 LEU cc_start: 0.8665 (tp) cc_final: 0.8393 (tm) REVERT: E 79 GLU cc_start: 0.8950 (tp30) cc_final: 0.8695 (tp30) REVERT: E 162 GLU cc_start: 0.8151 (tp30) cc_final: 0.7935 (tp30) REVERT: E 262 MET cc_start: 0.8054 (tmm) cc_final: 0.7779 (ttp) REVERT: E 461 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8579 (tm-30) REVERT: E 638 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8726 (mm-40) REVERT: E 713 MET cc_start: 0.8627 (mmm) cc_final: 0.8389 (mmm) REVERT: E 729 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8608 (m-80) REVERT: E 776 GLU cc_start: 0.9036 (pp20) cc_final: 0.8733 (pp20) REVERT: E 780 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8412 (mp0) outliers start: 44 outliers final: 9 residues processed: 246 average time/residue: 1.4079 time to fit residues: 386.2139 Evaluate side-chains 186 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS 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 206 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 184 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 738 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058924 restraints weight = 36051.591| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.03 r_work: 0.2815 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17129 Z= 0.255 Angle : 0.572 8.675 23510 Z= 0.281 Chirality : 0.041 0.147 2749 Planarity : 0.004 0.043 2817 Dihedral : 13.759 173.021 3139 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.31 % Allowed : 18.97 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 1990 helix: 2.06 (0.18), residues: 850 sheet: -0.35 (0.27), residues: 345 loop : 0.25 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 587 HIS 0.004 0.001 HIS F 381 PHE 0.012 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.005 0.000 ARG E 46 *********************** 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 249 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8603 (tptt) REVERT: B 64 ASP cc_start: 0.8770 (t0) cc_final: 0.8501 (t0) REVERT: B 160 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: B 226 ARG cc_start: 0.8668 (ppt170) cc_final: 0.8302 (ppt170) REVERT: C 64 ASP cc_start: 0.8870 (t0) cc_final: 0.8630 (t0) REVERT: C 70 ASP cc_start: 0.8562 (m-30) cc_final: 0.8318 (m-30) REVERT: C 229 ASP cc_start: 0.8575 (t0) cc_final: 0.8300 (t0) REVERT: D 52 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8662 (tptp) REVERT: D 212 LYS cc_start: 0.8778 (tttt) cc_final: 0.8141 (tttp) REVERT: E 38 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7435 (mtp85) REVERT: E 60 LEU cc_start: 0.8692 (tp) cc_final: 0.8423 (tm) REVERT: E 79 GLU cc_start: 0.8927 (tp30) cc_final: 0.8644 (tp30) REVERT: E 162 GLU cc_start: 0.8200 (tp30) cc_final: 0.7966 (tp30) REVERT: E 262 MET cc_start: 0.8192 (tmm) cc_final: 0.7883 (ttp) REVERT: E 461 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8619 (tm-30) REVERT: E 608 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9183 (ttpp) REVERT: E 729 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8669 (m-80) REVERT: E 776 GLU cc_start: 0.9084 (pp20) cc_final: 0.8824 (pp20) REVERT: E 780 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8387 (mp0) REVERT: E 785 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8630 (ttp80) REVERT: F 99 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8698 (mm-30) REVERT: F 131 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8685 (mtmm) REVERT: F 217 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7452 (tpt90) outliers start: 54 outliers final: 16 residues processed: 239 average time/residue: 1.4137 time to fit residues: 375.5558 Evaluate side-chains 191 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 110 THR 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 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 699 GLU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 785 ARG Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 46 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 168 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 158 optimal weight: 0.3980 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 220 GLN E 96 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 HIS ** 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 = 0.3357 r_free = 0.3357 target = 0.079018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059289 restraints weight = 36504.746| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.06 r_work: 0.2822 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17129 Z= 0.228 Angle : 0.561 9.554 23510 Z= 0.275 Chirality : 0.041 0.149 2749 Planarity : 0.004 0.044 2817 Dihedral : 13.772 172.500 3139 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.31 % Allowed : 19.21 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 1990 helix: 2.04 (0.18), residues: 852 sheet: -0.38 (0.27), residues: 345 loop : 0.23 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.006 0.000 ARG E 43 *********************** 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 253 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8554 (tptt) REVERT: A 151 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8332 (mp) REVERT: B 64 ASP cc_start: 0.8780 (t0) cc_final: 0.8505 (t0) REVERT: B 160 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: B 226 ARG cc_start: 0.8686 (ppt170) cc_final: 0.8298 (ppt170) REVERT: B 251 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8868 (mm) REVERT: C 64 ASP cc_start: 0.8834 (t0) cc_final: 0.8597 (t0) REVERT: C 70 ASP cc_start: 0.8581 (m-30) cc_final: 0.8328 (m-30) REVERT: C 232 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8355 (mt-10) REVERT: D 52 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8638 (tptp) REVERT: D 212 LYS cc_start: 0.8782 (tttt) cc_final: 0.8098 (tttp) REVERT: E 38 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7396 (mtp85) REVERT: E 60 LEU cc_start: 0.8702 (tp) cc_final: 0.8423 (tm) REVERT: E 79 GLU cc_start: 0.8930 (tp30) cc_final: 0.8627 (tp30) REVERT: E 163 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8520 (mm) REVERT: E 262 MET cc_start: 0.8079 (tmm) cc_final: 0.7822 (ttp) REVERT: E 461 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8675 (tm-30) REVERT: E 608 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9169 (ttpp) REVERT: E 638 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8641 (mm-40) REVERT: E 713 MET cc_start: 0.8714 (mmm) cc_final: 0.8437 (mmm) REVERT: E 776 GLU cc_start: 0.9115 (pp20) cc_final: 0.8830 (pp20) REVERT: E 780 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: F 99 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8693 (mm-30) REVERT: F 131 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8689 (mtmm) REVERT: F 217 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7432 (tpt90) outliers start: 54 outliers final: 14 residues processed: 242 average time/residue: 1.4418 time to fit residues: 387.1459 Evaluate side-chains 194 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 2.493 ------------------------------------------------------------------------------- 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 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 206 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 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 638 GLN Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 188 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ** 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 = 0.3352 r_free = 0.3352 target = 0.078741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.059004 restraints weight = 36570.785| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.05 r_work: 0.2816 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17129 Z= 0.252 Angle : 0.581 10.424 23510 Z= 0.285 Chirality : 0.041 0.152 2749 Planarity : 0.004 0.044 2817 Dihedral : 13.780 172.176 3139 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.07 % Allowed : 19.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 1990 helix: 1.99 (0.18), residues: 850 sheet: -0.34 (0.27), residues: 360 loop : 0.23 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.003 0.000 ARG E 46 *********************** 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 233 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8537 (tptt) REVERT: A 151 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 64 ASP cc_start: 0.8779 (t0) cc_final: 0.8491 (t0) REVERT: B 160 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: B 226 ARG cc_start: 0.8692 (ppt170) cc_final: 0.8256 (ppt170) REVERT: B 251 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8850 (mm) REVERT: C 64 ASP cc_start: 0.8832 (t0) cc_final: 0.8605 (t0) REVERT: C 70 ASP cc_start: 0.8554 (m-30) cc_final: 0.8308 (m-30) REVERT: D 52 LYS cc_start: 0.8970 (ttmm) cc_final: 0.8650 (tptp) REVERT: D 212 LYS cc_start: 0.8757 (tttt) cc_final: 0.8125 (tttp) REVERT: E 38 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7352 (mtp85) REVERT: E 60 LEU cc_start: 0.8708 (tp) cc_final: 0.8423 (tm) REVERT: E 163 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8608 (mm) REVERT: E 262 MET cc_start: 0.8206 (tmm) cc_final: 0.7925 (ttp) REVERT: E 461 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8712 (tm-30) REVERT: E 608 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9178 (ttpp) REVERT: E 713 MET cc_start: 0.8666 (mmm) cc_final: 0.8420 (mmm) REVERT: E 776 GLU cc_start: 0.9101 (pp20) cc_final: 0.8823 (pp20) REVERT: E 780 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: F 99 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8658 (mm-30) REVERT: F 100 MET cc_start: 0.8824 (ppp) cc_final: 0.8527 (ppp) REVERT: F 131 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8681 (mtmm) REVERT: F 217 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7402 (tpt90) outliers start: 50 outliers final: 14 residues processed: 221 average time/residue: 1.3507 time to fit residues: 333.2097 Evaluate side-chains 190 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 251 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 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 F residue 111 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 203 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 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 ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 HIS ** 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 = 0.3351 r_free = 0.3351 target = 0.078821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059303 restraints weight = 36056.608| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.04 r_work: 0.2824 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17129 Z= 0.243 Angle : 0.581 10.023 23510 Z= 0.285 Chirality : 0.041 0.151 2749 Planarity : 0.004 0.043 2817 Dihedral : 13.789 172.032 3139 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.76 % Allowed : 21.06 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 1990 helix: 1.99 (0.18), residues: 854 sheet: -0.35 (0.27), residues: 360 loop : 0.22 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.003 0.000 ARG C 116 *********************** 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 233 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8580 (tptt) REVERT: A 151 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8364 (mp) REVERT: B 64 ASP cc_start: 0.8773 (t0) cc_final: 0.8501 (t0) REVERT: B 160 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: B 226 ARG cc_start: 0.8720 (ppt170) cc_final: 0.8298 (ppt170) REVERT: B 251 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8851 (mm) REVERT: C 64 ASP cc_start: 0.8828 (t0) cc_final: 0.8608 (t0) REVERT: C 70 ASP cc_start: 0.8597 (m-30) cc_final: 0.8359 (m-30) REVERT: D 48 GLU cc_start: 0.8160 (pm20) cc_final: 0.7902 (pm20) REVERT: D 52 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8706 (tptp) REVERT: D 212 LYS cc_start: 0.8737 (tttt) cc_final: 0.8004 (pptt) REVERT: E 38 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7329 (mtp85) REVERT: E 60 LEU cc_start: 0.8739 (tp) cc_final: 0.8464 (tm) REVERT: E 162 GLU cc_start: 0.8093 (tp30) cc_final: 0.7807 (tp30) REVERT: E 608 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9177 (ttpp) REVERT: E 713 MET cc_start: 0.8739 (mmm) cc_final: 0.8462 (mmm) REVERT: E 776 GLU cc_start: 0.9084 (pp20) cc_final: 0.8801 (pp20) REVERT: E 780 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: F 99 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8671 (mm-30) REVERT: F 217 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7448 (tpt90) outliers start: 45 outliers final: 17 residues processed: 220 average time/residue: 1.3659 time to fit residues: 335.0080 Evaluate side-chains 200 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 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 122 SER Chi-restraints excluded: chain E residue 416 MET 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 745 VAL 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 25 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN D 260 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 = 0.078580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059013 restraints weight = 35891.692| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.03 r_work: 0.2818 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17129 Z= 0.259 Angle : 0.599 10.527 23510 Z= 0.294 Chirality : 0.041 0.154 2749 Planarity : 0.004 0.044 2817 Dihedral : 13.813 173.207 3139 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.58 % Allowed : 21.79 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1990 helix: 2.02 (0.18), residues: 845 sheet: -0.38 (0.27), residues: 360 loop : 0.19 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.005 0.000 ARG E 43 *********************** 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 222 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8576 (tptt) REVERT: B 64 ASP cc_start: 0.8771 (t0) cc_final: 0.8496 (t0) REVERT: B 160 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: B 251 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8858 (mm) REVERT: C 64 ASP cc_start: 0.8842 (t0) cc_final: 0.8613 (t0) REVERT: C 70 ASP cc_start: 0.8602 (m-30) cc_final: 0.8364 (m-30) REVERT: C 229 ASP cc_start: 0.8477 (t0) cc_final: 0.8245 (t0) REVERT: D 52 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8710 (tptp) REVERT: D 212 LYS cc_start: 0.8723 (tttt) cc_final: 0.7988 (pptt) REVERT: E 38 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7302 (mtp85) REVERT: E 60 LEU cc_start: 0.8737 (tp) cc_final: 0.8439 (tm) REVERT: E 162 GLU cc_start: 0.8165 (tp30) cc_final: 0.7895 (tp30) REVERT: E 163 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8580 (mm) REVERT: E 608 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9180 (ttpp) REVERT: E 654 VAL cc_start: 0.8986 (t) cc_final: 0.8723 (p) REVERT: E 713 MET cc_start: 0.8761 (mmm) cc_final: 0.8500 (mmm) REVERT: E 776 GLU cc_start: 0.9078 (pp20) cc_final: 0.8786 (pp20) REVERT: E 780 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: F 99 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8673 (mm-30) REVERT: F 217 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7453 (tpt90) outliers start: 42 outliers final: 17 residues processed: 209 average time/residue: 1.3074 time to fit residues: 305.8560 Evaluate side-chains 197 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.993 ------------------------------------------------------------------------------- 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 200 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 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 745 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 87 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** E 505 ASN ** 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 = 0.3364 r_free = 0.3364 target = 0.079333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059809 restraints weight = 36242.155| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.04 r_work: 0.2836 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17129 Z= 0.216 Angle : 0.593 10.788 23510 Z= 0.289 Chirality : 0.041 0.150 2749 Planarity : 0.004 0.043 2817 Dihedral : 13.804 177.654 3139 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.03 % Allowed : 22.34 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 1990 helix: 2.07 (0.18), residues: 845 sheet: -0.40 (0.27), residues: 360 loop : 0.15 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.010 0.000 ARG E 43 *********************** 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 222 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8548 (tptt) REVERT: B 64 ASP cc_start: 0.8766 (t0) cc_final: 0.8501 (t0) REVERT: B 160 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: B 226 ARG cc_start: 0.8710 (ppt170) cc_final: 0.8302 (ppt170) REVERT: B 251 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8840 (mm) REVERT: C 64 ASP cc_start: 0.8837 (t0) cc_final: 0.8634 (t0) REVERT: C 70 ASP cc_start: 0.8606 (m-30) cc_final: 0.8369 (m-30) REVERT: D 52 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8714 (tptp) REVERT: D 212 LYS cc_start: 0.8729 (tttt) cc_final: 0.8004 (pptt) REVERT: E 38 ARG cc_start: 0.7683 (mtp85) cc_final: 0.7318 (mtp85) REVERT: E 147 TYR cc_start: 0.8766 (t80) cc_final: 0.8563 (t80) REVERT: E 163 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8599 (mm) REVERT: E 461 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8714 (tm-30) REVERT: E 579 VAL cc_start: 0.8938 (t) cc_final: 0.8706 (m) REVERT: E 608 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9173 (ttpp) REVERT: E 654 VAL cc_start: 0.8951 (t) cc_final: 0.8683 (p) REVERT: E 713 MET cc_start: 0.8695 (mmm) cc_final: 0.8462 (mmm) REVERT: E 776 GLU cc_start: 0.9083 (pp20) cc_final: 0.8753 (pp20) REVERT: E 780 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: F 99 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8645 (mm-30) REVERT: F 217 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7421 (tpt90) outliers start: 33 outliers final: 18 residues processed: 211 average time/residue: 1.3863 time to fit residues: 326.0828 Evaluate side-chains 200 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 200 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 C residue 229 ASP Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 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 176 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 169 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** E 527 HIS ** 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 = 0.3346 r_free = 0.3346 target = 0.078338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058824 restraints weight = 36054.599| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.02 r_work: 0.2814 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17129 Z= 0.289 Angle : 0.625 12.111 23510 Z= 0.306 Chirality : 0.042 0.158 2749 Planarity : 0.004 0.044 2817 Dihedral : 13.831 177.234 3139 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.60 % Allowed : 23.27 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1990 helix: 2.00 (0.18), residues: 843 sheet: -0.40 (0.27), residues: 360 loop : 0.10 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 587 HIS 0.003 0.001 HIS A 109 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.007 0.000 ARG E 675 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8594 (tptt) REVERT: B 64 ASP cc_start: 0.8784 (t0) cc_final: 0.8506 (t0) REVERT: B 69 LYS cc_start: 0.8847 (tmmm) cc_final: 0.8643 (tmmm) REVERT: B 160 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: B 251 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8856 (mm) REVERT: C 64 ASP cc_start: 0.8842 (t0) cc_final: 0.8627 (t0) REVERT: C 70 ASP cc_start: 0.8615 (m-30) cc_final: 0.8383 (m-30) REVERT: D 52 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8734 (tptp) REVERT: D 212 LYS cc_start: 0.8731 (tttt) cc_final: 0.8025 (pptt) REVERT: E 38 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7342 (mtp85) REVERT: E 608 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9194 (ttpp) REVERT: E 654 VAL cc_start: 0.9001 (t) cc_final: 0.8741 (p) REVERT: E 713 MET cc_start: 0.8742 (mmm) cc_final: 0.8505 (mmm) REVERT: E 776 GLU cc_start: 0.9112 (pp20) cc_final: 0.8842 (pp20) REVERT: E 780 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: F 99 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8639 (mm-30) REVERT: F 217 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7478 (tpt90) outliers start: 26 outliers final: 16 residues processed: 196 average time/residue: 1.3491 time to fit residues: 295.2959 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 : 2.088 ------------------------------------------------------------------------------- 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 200 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 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 416 MET 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 49 optimal weight: 0.9990 chunk 183 optimal weight: 0.0370 chunk 189 optimal weight: 0.0970 chunk 102 optimal weight: 0.6980 chunk 188 optimal weight: 0.9980 chunk 134 optimal weight: 0.3980 chunk 43 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 121 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 overall best weight: 0.2056 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.080864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061444 restraints weight = 36085.656| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.04 r_work: 0.2876 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17129 Z= 0.172 Angle : 0.597 12.251 23510 Z= 0.290 Chirality : 0.041 0.149 2749 Planarity : 0.004 0.042 2817 Dihedral : 13.740 173.552 3139 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.41 % Allowed : 23.76 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 1990 helix: 2.08 (0.18), residues: 854 sheet: -0.31 (0.27), residues: 356 loop : 0.12 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 587 HIS 0.002 0.000 HIS E 342 PHE 0.012 0.001 PHE E 521 TYR 0.011 0.001 TYR E 59 ARG 0.008 0.000 ARG E 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11874.19 seconds wall clock time: 211 minutes 14.28 seconds (12674.28 seconds total)