Starting phenix.real_space_refine on Sat Jun 14 21:53:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey0_50050/06_2025/9ey0_50050.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey0_50050/06_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_50050/06_2025/9ey0_50050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey0_50050/06_2025/9ey0_50050.map" model { file = "/net/cci-nas-00/data/ceres_data/9ey0_50050/06_2025/9ey0_50050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey0_50050/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.10, per 1000 atoms: 0.67 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: 4.26 Conformation dependent library (CDL) restraints added in 2.0 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: 5.85 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: 6.48 Time building geometry restraints manager: 5.05 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 48.310 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.286 17135 Z= 0.272 Angle : 0.559 13.287 23510 Z= 0.305 Chirality : 0.041 0.324 2749 Planarity : 0.003 0.037 2817 Dihedral : 17.624 175.758 6778 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.18 % Allowed : 18.66 % Favored : 81.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.22334 ( 775) hydrogen bonds : angle 8.07919 ( 2203) metal coordination : bond 0.26388 ( 5) covalent geometry : bond 0.00454 (17129) covalent geometry : angle 0.55857 (23510) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 1.848 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: 1.3214 time to fit residues: 281.4625 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 : 1.998 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059729 restraints weight = 35952.087| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.03 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: 0.8674 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 17135 Z= 0.152 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 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 775) hydrogen bonds : angle 5.38534 ( 2203) metal coordination : bond 0.00613 ( 5) covalent geometry : bond 0.00361 (17129) covalent geometry : angle 0.56977 (23510) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ARG cc_start: 0.8665 (ppt170) cc_final: 0.8207 (ppt170) REVERT: C 64 ASP cc_start: 0.8871 (t0) cc_final: 0.8582 (t0) REVERT: C 70 ASP cc_start: 0.8607 (m-30) cc_final: 0.8403 (m-30) REVERT: D 179 THR cc_start: 0.9163 (t) cc_final: 0.8898 (m) REVERT: D 211 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7831 (tm-30) REVERT: E 38 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7494 (mtp85) REVERT: E 60 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8431 (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: 1.3183 time to fit residues: 349.2544 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 : 1.858 ------------------------------------------------------------------------------- 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: 0.1980 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: 0.0770 chunk 170 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5340 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.079284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.059422 restraints weight = 36164.207| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.04 r_work: 0.2828 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17135 Z= 0.141 Angle : 0.546 8.526 23510 Z= 0.271 Chirality : 0.041 0.145 2749 Planarity : 0.004 0.040 2817 Dihedral : 13.720 175.007 3139 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.76 % Allowed : 18.29 % Favored : 78.94 % 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: 1.40 (0.19), residues: 1990 helix: 2.12 (0.18), residues: 849 sheet: -0.22 (0.28), residues: 343 loop : 0.28 (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 F 381 PHE 0.011 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.008 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 775) hydrogen bonds : angle 4.99994 ( 2203) metal coordination : bond 0.00261 ( 5) covalent geometry : bond 0.00336 (17129) covalent geometry : angle 0.54632 (23510) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8621 (tptt) REVERT: B 64 ASP cc_start: 0.8728 (t0) cc_final: 0.8489 (t0) REVERT: B 160 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: B 226 ARG cc_start: 0.8636 (ppt170) cc_final: 0.8324 (ppt170) REVERT: C 64 ASP cc_start: 0.8869 (t0) cc_final: 0.8530 (t0) REVERT: C 70 ASP cc_start: 0.8543 (m-30) cc_final: 0.8329 (m-30) REVERT: C 140 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: D 160 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: E 60 LEU cc_start: 0.8672 (tp) cc_final: 0.8399 (tm) REVERT: E 79 GLU cc_start: 0.8946 (tp30) cc_final: 0.8689 (tp30) REVERT: E 162 GLU cc_start: 0.8144 (tp30) cc_final: 0.7933 (tp30) REVERT: E 262 MET cc_start: 0.8052 (tmm) cc_final: 0.7799 (ttp) REVERT: E 461 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8615 (tm-30) REVERT: E 638 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8720 (mm-40) REVERT: E 713 MET cc_start: 0.8629 (mmm) cc_final: 0.8398 (mmm) REVERT: E 776 GLU cc_start: 0.9041 (pp20) cc_final: 0.8735 (pp20) REVERT: E 780 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8392 (mp0) outliers start: 45 outliers final: 9 residues processed: 248 average time/residue: 1.4827 time to fit residues: 408.8418 Evaluate side-chains 185 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 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 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: 0.7980 chunk 139 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.0770 chunk 148 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3369 r_free = 0.3369 target = 0.079653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059894 restraints weight = 36001.803| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.04 r_work: 0.2840 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17135 Z= 0.126 Angle : 0.552 8.652 23510 Z= 0.270 Chirality : 0.041 0.148 2749 Planarity : 0.004 0.042 2817 Dihedral : 13.716 173.550 3139 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.38 % Allowed : 19.09 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.19), residues: 1990 helix: 2.13 (0.18), residues: 849 sheet: -0.31 (0.27), residues: 343 loop : 0.26 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.011 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.005 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 775) hydrogen bonds : angle 4.82249 ( 2203) metal coordination : bond 0.00210 ( 5) covalent geometry : bond 0.00302 (17129) covalent geometry : angle 0.55208 (23510) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8771 (t0) cc_final: 0.8485 (t0) REVERT: B 160 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: B 226 ARG cc_start: 0.8657 (ppt170) cc_final: 0.8300 (ppt170) REVERT: C 64 ASP cc_start: 0.8862 (t0) cc_final: 0.8507 (t0) REVERT: C 70 ASP cc_start: 0.8543 (m-30) cc_final: 0.8300 (m-30) REVERT: D 52 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8687 (tptp) REVERT: D 212 LYS cc_start: 0.8768 (tttt) cc_final: 0.7990 (pptt) REVERT: E 38 ARG cc_start: 0.7713 (mtp85) cc_final: 0.7403 (mtp85) REVERT: E 60 LEU cc_start: 0.8682 (tp) cc_final: 0.8412 (tm) REVERT: E 79 GLU cc_start: 0.8944 (tp30) cc_final: 0.8662 (tp30) REVERT: E 163 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8467 (mm) REVERT: E 262 MET cc_start: 0.8147 (tmm) cc_final: 0.7841 (ttp) REVERT: E 461 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8656 (tm-30) REVERT: E 608 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9172 (ttpp) REVERT: E 729 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: E 776 GLU cc_start: 0.9059 (pp20) cc_final: 0.8807 (pp20) REVERT: E 780 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: E 785 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8642 (ttp80) REVERT: F 99 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8670 (mm-30) REVERT: F 217 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7393 (tpt90) outliers start: 55 outliers final: 14 residues processed: 243 average time/residue: 1.3757 time to fit residues: 371.9193 Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 709 ILE 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 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: 0.8980 chunk 133 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 168 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 158 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 96 GLN ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.059546 restraints weight = 36495.025| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.05 r_work: 0.2831 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17135 Z= 0.140 Angle : 0.561 9.656 23510 Z= 0.274 Chirality : 0.041 0.148 2749 Planarity : 0.004 0.042 2817 Dihedral : 13.727 172.754 3139 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.19 % Allowed : 19.83 % Favored : 76.98 % 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: 1.32 (0.19), residues: 1990 helix: 2.10 (0.18), residues: 853 sheet: -0.39 (0.27), residues: 345 loop : 0.23 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.012 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.004 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 775) hydrogen bonds : angle 4.80038 ( 2203) metal coordination : bond 0.00227 ( 5) covalent geometry : bond 0.00340 (17129) covalent geometry : angle 0.56074 (23510) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8341 (mp) REVERT: B 64 ASP cc_start: 0.8763 (t0) cc_final: 0.8476 (t0) REVERT: B 160 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: B 226 ARG cc_start: 0.8680 (ppt170) cc_final: 0.8296 (ppt170) REVERT: C 64 ASP cc_start: 0.8874 (t0) cc_final: 0.8622 (t0) REVERT: C 70 ASP cc_start: 0.8551 (m-30) cc_final: 0.8338 (m-30) REVERT: D 48 GLU cc_start: 0.8143 (pm20) cc_final: 0.7889 (pm20) REVERT: D 52 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8674 (tptp) REVERT: D 212 LYS cc_start: 0.8768 (tttt) cc_final: 0.7999 (pptt) REVERT: E 38 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7361 (mtp85) REVERT: E 60 LEU cc_start: 0.8692 (tp) cc_final: 0.8413 (tm) REVERT: E 79 GLU cc_start: 0.8913 (tp30) cc_final: 0.8618 (tp30) REVERT: E 162 GLU cc_start: 0.8023 (tp30) cc_final: 0.7712 (tp30) REVERT: E 163 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8451 (mm) REVERT: E 262 MET cc_start: 0.8104 (tmm) cc_final: 0.7839 (ttp) REVERT: E 461 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8698 (tm-30) REVERT: E 608 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9173 (ttpp) REVERT: E 638 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8614 (mm-40) REVERT: E 713 MET cc_start: 0.8705 (mmm) cc_final: 0.8452 (mmm) REVERT: E 776 GLU cc_start: 0.9090 (pp20) cc_final: 0.8817 (pp20) REVERT: E 780 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: F 99 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8656 (mm-30) REVERT: F 217 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7399 (tpt90) outliers start: 52 outliers final: 13 residues processed: 238 average time/residue: 1.3248 time to fit residues: 350.5245 Evaluate side-chains 195 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 638 GLN 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 300 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 chunk 160 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 chunk 188 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059994 restraints weight = 36445.505| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.06 r_work: 0.2840 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17135 Z= 0.127 Angle : 0.562 10.314 23510 Z= 0.276 Chirality : 0.041 0.150 2749 Planarity : 0.004 0.043 2817 Dihedral : 13.712 172.515 3139 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.39 % Allowed : 20.50 % Favored : 77.10 % 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: 1.35 (0.19), residues: 1990 helix: 2.10 (0.18), residues: 852 sheet: -0.27 (0.27), residues: 358 loop : 0.23 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.012 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.003 0.000 ARG E 785 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 775) hydrogen bonds : angle 4.73312 ( 2203) metal coordination : bond 0.00209 ( 5) covalent geometry : bond 0.00306 (17129) covalent geometry : angle 0.56212 (23510) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 1.881 Fit side-chains revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8755 (t0) cc_final: 0.8463 (t0) REVERT: B 160 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: B 226 ARG cc_start: 0.8685 (ppt170) cc_final: 0.8295 (ppt170) REVERT: C 64 ASP cc_start: 0.8883 (t0) cc_final: 0.8637 (t0) REVERT: C 70 ASP cc_start: 0.8537 (m-30) cc_final: 0.8287 (m-30) REVERT: D 52 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8627 (tptp) REVERT: D 212 LYS cc_start: 0.8737 (tttt) cc_final: 0.8001 (pptt) REVERT: E 38 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7295 (mtp85) REVERT: E 60 LEU cc_start: 0.8694 (tp) cc_final: 0.8409 (tm) REVERT: E 79 GLU cc_start: 0.8908 (tp30) cc_final: 0.8698 (tp30) REVERT: E 457 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8365 (tm-30) REVERT: E 461 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8707 (tm-30) REVERT: E 608 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9172 (ttpp) REVERT: E 713 MET cc_start: 0.8680 (mmm) cc_final: 0.8431 (mmm) REVERT: E 729 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8632 (m-80) REVERT: E 776 GLU cc_start: 0.9068 (pp20) cc_final: 0.8793 (pp20) REVERT: E 780 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: F 99 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8646 (mm-30) REVERT: F 217 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7394 (tpt90) outliers start: 39 outliers final: 14 residues processed: 220 average time/residue: 1.2854 time to fit residues: 316.7095 Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL 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 587 TRP Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 709 ILE Chi-restraints excluded: chain E residue 729 TYR 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 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.078490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058959 restraints weight = 36072.790| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.04 r_work: 0.2815 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17135 Z= 0.173 Angle : 0.595 11.031 23510 Z= 0.291 Chirality : 0.042 0.156 2749 Planarity : 0.004 0.044 2817 Dihedral : 13.771 171.771 3139 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.64 % Allowed : 21.55 % Favored : 75.81 % 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: 845 sheet: -0.30 (0.27), residues: 360 loop : 0.21 (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 39 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.003 0.000 ARG E 785 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 775) hydrogen bonds : angle 4.82562 ( 2203) metal coordination : bond 0.00316 ( 5) covalent geometry : bond 0.00421 (17129) covalent geometry : angle 0.59518 (23510) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8780 (t0) cc_final: 0.8522 (t0) REVERT: B 160 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: B 226 ARG cc_start: 0.8713 (ppt170) cc_final: 0.8301 (ppt170) REVERT: C 64 ASP cc_start: 0.8868 (t0) cc_final: 0.8650 (t0) REVERT: C 70 ASP cc_start: 0.8605 (m-30) cc_final: 0.8373 (m-30) REVERT: D 52 LYS cc_start: 0.9035 (ttmm) cc_final: 0.8718 (tptp) REVERT: D 212 LYS cc_start: 0.8745 (tttt) cc_final: 0.8019 (pptt) REVERT: E 38 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7286 (mtp85) REVERT: E 60 LEU cc_start: 0.8723 (tp) cc_final: 0.8446 (tm) REVERT: E 79 GLU cc_start: 0.8899 (tp30) cc_final: 0.8686 (tp30) REVERT: E 162 GLU cc_start: 0.8069 (tp30) cc_final: 0.7835 (tp30) REVERT: E 163 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8559 (mm) REVERT: E 262 MET cc_start: 0.8047 (tmm) cc_final: 0.7827 (ttp) REVERT: E 457 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8414 (tm-30) REVERT: E 461 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8711 (tm-30) REVERT: E 608 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9181 (ttpp) REVERT: E 776 GLU cc_start: 0.9066 (pp20) cc_final: 0.8800 (pp20) REVERT: E 780 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: F 99 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8642 (mm-30) REVERT: F 217 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7493 (tpt90) outliers start: 43 outliers final: 14 residues processed: 215 average time/residue: 1.4606 time to fit residues: 349.1583 Evaluate side-chains 187 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL 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 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 780 GLU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059171 restraints weight = 36079.381| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.04 r_work: 0.2822 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17135 Z= 0.165 Angle : 0.606 10.644 23510 Z= 0.296 Chirality : 0.041 0.155 2749 Planarity : 0.004 0.044 2817 Dihedral : 13.791 171.790 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 : 2.33 % Allowed : 22.04 % 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: 2.05 (0.18), residues: 843 sheet: -0.37 (0.27), residues: 360 loop : 0.17 (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 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 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 775) hydrogen bonds : angle 4.80553 ( 2203) metal coordination : bond 0.00312 ( 5) covalent geometry : bond 0.00404 (17129) covalent geometry : angle 0.60621 (23510) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8783 (t0) cc_final: 0.8495 (t0) REVERT: B 160 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8077 (pm20) REVERT: C 64 ASP cc_start: 0.8817 (t0) cc_final: 0.8578 (t0) REVERT: C 232 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8366 (mt-10) REVERT: D 52 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8700 (tptp) REVERT: D 212 LYS cc_start: 0.8741 (tttt) cc_final: 0.8031 (pptt) REVERT: E 38 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7295 (mtp85) REVERT: E 79 GLU cc_start: 0.8917 (tp30) cc_final: 0.8687 (tp30) REVERT: E 162 GLU cc_start: 0.8113 (tp30) cc_final: 0.7848 (tp30) REVERT: E 163 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8552 (mm) REVERT: E 262 MET cc_start: 0.8006 (tmm) cc_final: 0.7759 (ttp) REVERT: E 457 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8407 (tm-30) REVERT: E 461 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8711 (tm-30) REVERT: E 608 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9181 (ttpp) REVERT: E 776 GLU cc_start: 0.9095 (pp20) cc_final: 0.8836 (pp20) REVERT: E 780 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: F 99 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8658 (mm-30) REVERT: F 217 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7447 (tpt90) outliers start: 38 outliers final: 16 residues processed: 211 average time/residue: 1.2647 time to fit residues: 299.0171 Evaluate side-chains 198 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 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 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 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: 0.0770 chunk 55 optimal weight: 0.8980 chunk 92 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 638 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.080053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.060574 restraints weight = 36197.244| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.04 r_work: 0.2853 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17135 Z= 0.121 Angle : 0.593 11.553 23510 Z= 0.287 Chirality : 0.041 0.153 2749 Planarity : 0.004 0.043 2817 Dihedral : 13.748 175.214 3139 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.47 % Allowed : 23.20 % Favored : 75.32 % 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: 2.06 (0.18), residues: 851 sheet: -0.25 (0.27), residues: 351 loop : 0.13 (0.23), residues: 788 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 0.012 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.013 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 775) hydrogen bonds : angle 4.68579 ( 2203) metal coordination : bond 0.00198 ( 5) covalent geometry : bond 0.00290 (17129) covalent geometry : angle 0.59262 (23510) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8737 (t0) cc_final: 0.8457 (t0) REVERT: B 100 THR cc_start: 0.8847 (m) cc_final: 0.8546 (t) REVERT: B 160 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: B 226 ARG cc_start: 0.8719 (ppt170) cc_final: 0.8350 (ppt170) REVERT: C 64 ASP cc_start: 0.8882 (t0) cc_final: 0.8671 (t0) REVERT: C 232 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8389 (mt-10) REVERT: D 48 GLU cc_start: 0.8144 (pm20) cc_final: 0.7884 (pm20) REVERT: D 52 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8707 (tptp) REVERT: D 110 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.7507 (m) REVERT: D 212 LYS cc_start: 0.8713 (tttt) cc_final: 0.8029 (pptt) REVERT: E 79 GLU cc_start: 0.8912 (tp30) cc_final: 0.8686 (tp30) REVERT: E 163 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8580 (mm) REVERT: E 461 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8713 (tm-30) REVERT: E 512 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8792 (pp) REVERT: E 579 VAL cc_start: 0.8918 (t) cc_final: 0.8674 (m) REVERT: E 608 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9175 (ttpp) REVERT: E 776 GLU cc_start: 0.9071 (pp20) cc_final: 0.8687 (pp20) REVERT: E 780 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: F 99 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8649 (mm-30) REVERT: F 217 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7396 (tpt90) outliers start: 24 outliers final: 9 residues processed: 216 average time/residue: 1.7866 time to fit residues: 427.9380 Evaluate side-chains 189 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 608 LYS 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 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 176 optimal weight: 0.9990 chunk 194 optimal weight: 0.3980 chunk 201 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.078469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058940 restraints weight = 36145.091| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.03 r_work: 0.2814 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17135 Z= 0.184 Angle : 0.642 13.077 23510 Z= 0.314 Chirality : 0.042 0.159 2749 Planarity : 0.005 0.085 2817 Dihedral : 13.810 178.321 3139 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.53 % Allowed : 24.00 % Favored : 74.46 % 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: 1.19 (0.19), residues: 1990 helix: 1.99 (0.18), residues: 843 sheet: -0.36 (0.27), residues: 360 loop : 0.15 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 587 HIS 0.004 0.001 HIS E 98 PHE 0.014 0.001 PHE E 771 TYR 0.012 0.001 TYR E 59 ARG 0.007 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 775) hydrogen bonds : angle 4.81042 ( 2203) metal coordination : bond 0.00339 ( 5) covalent geometry : bond 0.00450 (17129) covalent geometry : angle 0.64176 (23510) Misc. bond : bond 0.00014 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 ASP cc_start: 0.8765 (t0) cc_final: 0.8491 (t0) REVERT: B 69 LYS cc_start: 0.8842 (tmmm) cc_final: 0.8632 (tmmm) REVERT: B 160 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: C 64 ASP cc_start: 0.8908 (t0) cc_final: 0.8670 (t0) REVERT: D 52 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8723 (tptp) REVERT: D 212 LYS cc_start: 0.8733 (tttt) cc_final: 0.8030 (pptt) REVERT: E 38 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7343 (mtp85) REVERT: E 461 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8635 (tm-30) REVERT: E 579 VAL cc_start: 0.8946 (t) cc_final: 0.8744 (m) REVERT: E 608 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9207 (ttpp) REVERT: E 654 VAL cc_start: 0.9014 (t) cc_final: 0.8751 (p) REVERT: E 776 GLU cc_start: 0.9120 (pp20) cc_final: 0.8843 (pp20) REVERT: E 780 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: F 99 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8652 (mm-30) REVERT: F 217 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7441 (tpt90) outliers start: 25 outliers final: 16 residues processed: 194 average time/residue: 1.2572 time to fit residues: 273.4609 Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 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 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 43 ARG Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 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: 0.5980 chunk 183 optimal weight: 0.0030 chunk 189 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 43 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 88 optimal weight: 0.0470 overall best weight: 0.2466 ------------------------------------------------------------------------------- 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 D 260 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.061178 restraints weight = 35906.271| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.04 r_work: 0.2869 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17135 Z= 0.117 Angle : 0.618 12.934 23510 Z= 0.300 Chirality : 0.041 0.151 2749 Planarity : 0.004 0.068 2817 Dihedral : 13.743 174.769 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 : 1.35 % Allowed : 24.62 % Favored : 74.03 % 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: 1.26 (0.19), residues: 1990 helix: 2.03 (0.18), residues: 852 sheet: -0.22 (0.27), residues: 341 loop : 0.11 (0.23), residues: 797 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 0.012 0.001 PHE E 521 TYR 0.011 0.001 TYR E 59 ARG 0.008 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 775) hydrogen bonds : angle 4.68053 ( 2203) metal coordination : bond 0.00162 ( 5) covalent geometry : bond 0.00278 (17129) covalent geometry : angle 0.61783 (23510) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13294.13 seconds wall clock time: 231 minutes 50.39 seconds (13910.39 seconds total)