Starting phenix.real_space_refine on Tue Dec 31 20:19:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey0_50050/12_2024/9ey0_50050.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey0_50050/12_2024/9ey0_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_50050/12_2024/9ey0_50050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey0_50050/12_2024/9ey0_50050.map" model { file = "/net/cci-nas-00/data/ceres_data/9ey0_50050/12_2024/9ey0_50050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey0_50050/12_2024/9ey0_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-5532/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: 11.14, 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: 4.49 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 546 " pdb="ZN ZN E 901 " - pdb=" ND1 HIS E 548 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 644 " pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 551 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 724 " 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 15 sheets defined 50.5% alpha, 12.8% beta 16 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 5.71 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: 6.40 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2686 1.31 - 1.44: 4536 1.44 - 1.57: 9634 1.57 - 1.69: 135 1.69 - 1.82: 138 Bond restraints: 17129 Sorted by residual: bond pdb=" C2' GTP T 101 " pdb=" C3' GTP T 101 " ideal model delta sigma weight residual 1.524 1.238 0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C1' GTP T 101 " pdb=" N9 GTP T 101 " ideal model delta sigma weight residual 1.475 1.320 0.155 2.00e-02 2.50e+03 6.01e+01 bond pdb=" CA PHE F 97 " pdb=" C PHE F 97 " ideal model delta sigma weight residual 1.523 1.624 -0.101 1.35e-02 5.49e+03 5.59e+01 bond pdb=" C3' GTP T 101 " pdb=" C4' GTP T 101 " ideal model delta sigma weight residual 1.524 1.661 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C5 GTP T 101 " pdb=" C6 GTP T 101 " ideal model delta sigma weight residual 1.390 1.525 -0.135 2.00e-02 2.50e+03 4.57e+01 ... (remaining 17124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 23286 2.66 - 5.31: 196 5.31 - 7.97: 21 7.97 - 10.63: 6 10.63 - 13.29: 1 Bond angle restraints: 23510 Sorted by residual: angle pdb=" N ILE F 98 " pdb=" CA ILE F 98 " pdb=" C ILE F 98 " ideal model delta sigma weight residual 110.62 123.91 -13.29 1.02e+00 9.61e-01 1.70e+02 angle pdb=" N VAL D 213 " pdb=" CA VAL D 213 " pdb=" C VAL D 213 " ideal model delta sigma weight residual 110.42 118.94 -8.52 9.60e-01 1.09e+00 7.87e+01 angle pdb=" N GLU F 96 " pdb=" CA GLU F 96 " pdb=" C GLU F 96 " ideal model delta sigma weight residual 112.23 101.87 10.36 1.26e+00 6.30e-01 6.76e+01 angle pdb=" N ILE F 98 " pdb=" CA ILE F 98 " pdb=" CB ILE F 98 " ideal model delta sigma weight residual 110.54 102.69 7.85 1.36e+00 5.41e-01 3.33e+01 angle pdb=" CA PHE F 97 " pdb=" C PHE F 97 " pdb=" N ILE F 98 " ideal model delta sigma weight residual 117.22 110.57 6.65 1.17e+00 7.31e-01 3.23e+01 ... (remaining 23505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 9983 35.15 - 70.30: 401 70.30 - 105.46: 49 105.46 - 140.61: 3 140.61 - 175.76: 2 Dihedral angle restraints: 10438 sinusoidal: 4742 harmonic: 5696 Sorted by residual: dihedral pdb=" O4' C T 44 " pdb=" C1' C T 44 " pdb=" N1 C T 44 " pdb=" C2 C T 44 " ideal model delta sinusoidal sigma weight residual -128.00 46.84 -174.84 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O2G GTP T 101 " pdb=" O3B GTP T 101 " pdb=" PG GTP T 101 " pdb=" PB GTP T 101 " ideal model delta sinusoidal sigma weight residual 177.30 -6.94 -175.76 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3B GTP T 101 " pdb=" O3A GTP T 101 " pdb=" PB GTP T 101 " pdb=" PA GTP T 101 " ideal model delta sinusoidal sigma weight residual -68.92 43.19 -112.12 1 2.00e+01 2.50e-03 3.30e+01 ... (remaining 10435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2460 0.065 - 0.130: 275 0.130 - 0.195: 10 0.195 - 0.259: 3 0.259 - 0.324: 1 Chirality restraints: 2749 Sorted by residual: chirality pdb=" CA PHE F 97 " pdb=" N PHE F 97 " pdb=" C PHE F 97 " pdb=" CB PHE F 97 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C2' SAM F 501 " pdb=" C1' SAM F 501 " pdb=" C3' SAM F 501 " pdb=" O2' SAM F 501 " both_signs ideal model delta sigma weight residual False -2.76 -2.52 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE F 98 " pdb=" N ILE F 98 " pdb=" C ILE F 98 " pdb=" CB ILE F 98 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2746 not shown) Planarity restraints: 2817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 97 " -0.011 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C PHE F 97 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE F 97 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE F 98 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 180 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO C 181 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 776 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" CD GLU E 776 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU E 776 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU E 776 " -0.007 2.00e-02 2.50e+03 ... (remaining 2814 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 178 2.58 - 3.16: 13911 3.16 - 3.74: 27308 3.74 - 4.32: 39055 4.32 - 4.90: 63427 Nonbonded interactions: 143879 Sorted by model distance: nonbonded pdb=" OD2 ASP E 550 " pdb="ZN ZN E 902 " model vdw 1.995 2.230 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 902 " model vdw 1.996 2.230 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 901 " model vdw 2.004 2.230 nonbonded pdb=" O ALA E 549 " pdb=" OG1 THR E 553 " model vdw 2.066 3.040 nonbonded pdb=" OG1 THR E 285 " pdb=" OE1 GLU E 290 " model vdw 2.072 3.040 ... (remaining 143874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 47.340 Find NCS groups from input model: 0.380 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:14.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.286 17129 Z= 0.327 Angle : 0.559 13.287 23510 Z= 0.305 Chirality : 0.041 0.324 2749 Planarity : 0.003 0.037 2817 Dihedral : 17.624 175.758 6778 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.18 % Allowed : 18.66 % Favored : 81.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1990 helix: 2.22 (0.18), residues: 868 sheet: -0.09 (0.29), residues: 365 loop : 0.36 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 659 HIS 0.002 0.000 HIS E 546 PHE 0.007 0.001 PHE F 312 TYR 0.008 0.001 TYR D 101 ARG 0.003 0.000 ARG E 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 1.791 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: 1.3756 time to fit residues: 292.6339 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 : 1.782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17129 Z= 0.237 Angle : 0.570 7.518 23510 Z= 0.285 Chirality : 0.042 0.180 2749 Planarity : 0.004 0.043 2817 Dihedral : 13.661 179.361 3139 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.70 % Allowed : 17.07 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1990 helix: 2.19 (0.18), residues: 844 sheet: -0.11 (0.29), residues: 340 loop : 0.38 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 587 HIS 0.004 0.001 HIS E 342 PHE 0.013 0.001 PHE F 97 TYR 0.013 0.001 TYR E 59 ARG 0.011 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ARG cc_start: 0.8652 (ppt170) cc_final: 0.8249 (ppt170) REVERT: D 179 THR cc_start: 0.9151 (t) cc_final: 0.8896 (m) REVERT: E 38 ARG cc_start: 0.7375 (mtp85) cc_final: 0.7169 (mtp85) REVERT: E 608 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8971 (tppp) outliers start: 44 outliers final: 11 residues processed: 238 average time/residue: 1.3801 time to fit residues: 365.4080 Evaluate side-chains 176 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 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 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 0.0570 chunk 51 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- 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 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17129 Z= 0.408 Angle : 0.623 8.977 23510 Z= 0.310 Chirality : 0.044 0.160 2749 Planarity : 0.005 0.042 2817 Dihedral : 13.894 173.603 3139 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.31 % Allowed : 18.17 % Favored : 78.51 % 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: 1.17 (0.19), residues: 1990 helix: 1.84 (0.18), residues: 851 sheet: -0.29 (0.28), residues: 343 loop : 0.24 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 587 HIS 0.005 0.001 HIS F 381 PHE 0.014 0.002 PHE C 223 TYR 0.013 0.001 TYR E 59 ARG 0.008 0.001 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 ASP cc_start: 0.9047 (p0) cc_final: 0.8841 (p0) REVERT: B 160 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: B 251 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9034 (mm) REVERT: C 70 ASP cc_start: 0.8207 (m-30) cc_final: 0.7982 (m-30) REVERT: E 262 MET cc_start: 0.7485 (tmm) cc_final: 0.7244 (ttp) REVERT: E 608 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8991 (tppp) REVERT: E 713 MET cc_start: 0.8384 (mmm) cc_final: 0.8173 (mmm) REVERT: E 776 GLU cc_start: 0.8728 (pp20) cc_final: 0.8522 (pp20) REVERT: F 162 ASN cc_start: 0.7255 (m-40) cc_final: 0.7035 (m110) REVERT: F 217 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7414 (tpt90) outliers start: 54 outliers final: 21 residues processed: 231 average time/residue: 1.3954 time to fit residues: 358.2617 Evaluate side-chains 181 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 199 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 176 optimal weight: 0.0470 chunk 53 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17129 Z= 0.241 Angle : 0.565 8.529 23510 Z= 0.279 Chirality : 0.041 0.151 2749 Planarity : 0.004 0.044 2817 Dihedral : 13.872 172.880 3139 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.68 % Allowed : 18.85 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1990 helix: 1.98 (0.18), residues: 845 sheet: -0.43 (0.27), residues: 345 loop : 0.20 (0.23), residues: 800 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 0.013 0.001 TYR E 59 ARG 0.006 0.000 ARG E 43 *********************** 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 252 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 192 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8724 (tptt) REVERT: B 160 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8141 (pm20) REVERT: B 226 ARG cc_start: 0.8709 (ppt170) cc_final: 0.8401 (ppt170) REVERT: D 212 LYS cc_start: 0.8568 (tttt) cc_final: 0.8029 (tttp) REVERT: E 163 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8522 (mm) REVERT: E 262 MET cc_start: 0.7543 (tmm) cc_final: 0.7294 (ttp) REVERT: E 608 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8964 (tppp) REVERT: E 695 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: F 217 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7309 (tpt90) outliers start: 60 outliers final: 18 residues processed: 238 average time/residue: 1.3509 time to fit residues: 358.0387 Evaluate side-chains 190 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 143 GLN 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 D residue 237 VAL 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 587 TRP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 695 GLU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 199 MET 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 164 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 168 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 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 33 GLN B 220 GLN C 143 GLN ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17129 Z= 0.261 Angle : 0.579 9.657 23510 Z= 0.284 Chirality : 0.042 0.154 2749 Planarity : 0.004 0.045 2817 Dihedral : 13.867 172.284 3139 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.01 % Allowed : 20.07 % Favored : 76.92 % 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: 1.14 (0.19), residues: 1990 helix: 1.96 (0.18), residues: 848 sheet: -0.45 (0.27), residues: 345 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 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.004 0.000 ARG F 302 *********************** 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 236 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8734 (tptt) REVERT: B 160 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: C 229 ASP cc_start: 0.8413 (t0) cc_final: 0.8204 (t0) REVERT: D 212 LYS cc_start: 0.8585 (tttt) cc_final: 0.7998 (tttp) REVERT: E 163 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8522 (mm) REVERT: E 262 MET cc_start: 0.7609 (tmm) cc_final: 0.7352 (ttp) REVERT: E 608 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8969 (ttpp) REVERT: E 638 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8273 (tp40) REVERT: E 713 MET cc_start: 0.8366 (mmm) cc_final: 0.8091 (mmm) REVERT: F 217 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7320 (tpt90) outliers start: 49 outliers final: 20 residues processed: 225 average time/residue: 1.3836 time to fit residues: 347.1505 Evaluate side-chains 189 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain 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 D residue 237 VAL Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 638 GLN Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 285 ASP 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 66 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17129 Z= 0.254 Angle : 0.588 10.301 23510 Z= 0.288 Chirality : 0.042 0.169 2749 Planarity : 0.004 0.045 2817 Dihedral : 13.858 172.158 3139 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.25 % Allowed : 20.32 % Favored : 76.43 % 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: 1.13 (0.19), residues: 1990 helix: 1.94 (0.18), residues: 848 sheet: -0.43 (0.27), residues: 360 loop : 0.13 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.003 0.000 ARG F 302 *********************** 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 249 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8704 (tptt) REVERT: B 160 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: C 232 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8393 (mt-10) REVERT: D 212 LYS cc_start: 0.8572 (tttt) cc_final: 0.8002 (pptt) REVERT: E 262 MET cc_start: 0.7688 (tmm) cc_final: 0.7454 (ttp) REVERT: E 457 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8063 (tm-30) REVERT: E 608 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8976 (ttpp) REVERT: E 654 VAL cc_start: 0.8998 (t) cc_final: 0.8777 (p) REVERT: E 713 MET cc_start: 0.8364 (mmm) cc_final: 0.8126 (mmm) REVERT: F 217 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7265 (tpt90) outliers start: 53 outliers final: 21 residues processed: 235 average time/residue: 1.3662 time to fit residues: 357.6855 Evaluate side-chains 194 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 112 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 0.0980 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 96 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN E 738 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17129 Z= 0.231 Angle : 0.591 10.905 23510 Z= 0.291 Chirality : 0.041 0.170 2749 Planarity : 0.004 0.046 2817 Dihedral : 13.834 173.268 3139 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.82 % Allowed : 21.61 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1990 helix: 1.95 (0.18), residues: 850 sheet: -0.44 (0.27), residues: 360 loop : 0.17 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.003 0.000 ARG F 302 *********************** 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 236 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8697 (tptt) REVERT: B 160 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: C 232 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8425 (mt-10) REVERT: D 212 LYS cc_start: 0.8552 (tttt) cc_final: 0.7992 (pptt) REVERT: E 262 MET cc_start: 0.7691 (tmm) cc_final: 0.7454 (ttp) REVERT: E 309 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9098 (p) REVERT: E 457 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 608 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8969 (ttpp) REVERT: E 654 VAL cc_start: 0.8979 (t) cc_final: 0.8756 (p) REVERT: E 713 MET cc_start: 0.8369 (mmm) cc_final: 0.8115 (mmm) REVERT: F 217 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7245 (tpt90) outliers start: 46 outliers final: 19 residues processed: 224 average time/residue: 1.3346 time to fit residues: 333.4919 Evaluate side-chains 195 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 16 THR 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 122 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17129 Z= 0.268 Angle : 0.606 10.315 23510 Z= 0.297 Chirality : 0.042 0.180 2749 Planarity : 0.004 0.046 2817 Dihedral : 13.858 179.737 3139 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.70 % Allowed : 22.16 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 1990 helix: 1.89 (0.18), residues: 850 sheet: -0.44 (0.27), residues: 360 loop : 0.13 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 587 HIS 0.003 0.001 HIS E 342 PHE 0.013 0.001 PHE E 521 TYR 0.012 0.001 TYR E 59 ARG 0.003 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 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 225 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8714 (tptt) REVERT: B 160 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: B 251 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8971 (mm) REVERT: D 212 LYS cc_start: 0.8543 (tttt) cc_final: 0.8009 (pptt) REVERT: E 457 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8248 (tm-30) REVERT: E 608 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8974 (ttpp) REVERT: E 654 VAL cc_start: 0.8995 (t) cc_final: 0.8773 (p) REVERT: E 713 MET cc_start: 0.8370 (mmm) cc_final: 0.8137 (mmm) REVERT: F 217 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7257 (tpt90) outliers start: 44 outliers final: 22 residues processed: 214 average time/residue: 1.4709 time to fit residues: 352.8027 Evaluate side-chains 199 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 199 MET 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 188 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 110 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17129 Z= 0.275 Angle : 0.625 11.459 23510 Z= 0.305 Chirality : 0.042 0.196 2749 Planarity : 0.004 0.046 2817 Dihedral : 13.845 174.594 3139 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.46 % Allowed : 22.41 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 1990 helix: 1.85 (0.18), residues: 850 sheet: -0.42 (0.27), residues: 360 loop : 0.12 (0.23), residues: 780 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 0.006 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8710 (tptt) REVERT: B 160 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: B 251 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8964 (mm) REVERT: D 212 LYS cc_start: 0.8530 (tttt) cc_final: 0.8009 (pptt) REVERT: E 654 VAL cc_start: 0.9020 (t) cc_final: 0.8788 (p) REVERT: E 713 MET cc_start: 0.8346 (mmm) cc_final: 0.8132 (mmm) REVERT: F 217 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7259 (tpt90) outliers start: 40 outliers final: 24 residues processed: 216 average time/residue: 1.2653 time to fit residues: 306.7599 Evaluate side-chains 205 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 199 MET 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 193 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 0.3980 chunk 203 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17129 Z= 0.260 Angle : 0.630 12.051 23510 Z= 0.308 Chirality : 0.042 0.179 2749 Planarity : 0.004 0.046 2817 Dihedral : 13.831 173.552 3139 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.09 % Allowed : 23.02 % Favored : 74.89 % 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: 1.08 (0.19), residues: 1990 helix: 1.87 (0.18), residues: 850 sheet: -0.43 (0.27), residues: 360 loop : 0.12 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 587 HIS 0.002 0.001 HIS E 342 PHE 0.019 0.001 PHE E 771 TYR 0.012 0.001 TYR E 59 ARG 0.009 0.000 ARG E 43 ********************** 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 216 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8706 (tptt) REVERT: B 160 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: D 212 LYS cc_start: 0.8517 (tttt) cc_final: 0.8008 (pptt) REVERT: E 654 VAL cc_start: 0.9023 (t) cc_final: 0.8791 (p) REVERT: F 217 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7252 (tpt90) outliers start: 34 outliers final: 24 residues processed: 207 average time/residue: 1.3910 time to fit residues: 325.9628 Evaluate side-chains 192 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 617 SER Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 199 MET 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 172 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 166 optimal weight: 0.5980 chunk 20 optimal weight: 0.0570 chunk 29 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 143 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3355 r_free = 0.3355 target = 0.078853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059484 restraints weight = 36197.497| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.04 r_work: 0.2827 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17129 Z= 0.234 Angle : 0.620 12.203 23510 Z= 0.303 Chirality : 0.042 0.159 2749 Planarity : 0.004 0.046 2817 Dihedral : 13.807 174.131 3139 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.90 % Allowed : 23.51 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.19), residues: 1990 helix: 1.90 (0.18), residues: 850 sheet: -0.41 (0.27), residues: 360 loop : 0.13 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 587 HIS 0.002 0.001 HIS E 39 PHE 0.013 0.001 PHE E 771 TYR 0.012 0.001 TYR E 59 ARG 0.007 0.000 ARG E 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5926.44 seconds wall clock time: 107 minutes 58.57 seconds (6478.57 seconds total)