Starting phenix.real_space_refine on Sun Aug 24 03:44:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey1_50051/08_2025/9ey1_50051.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey1_50051/08_2025/9ey1_50051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ey1_50051/08_2025/9ey1_50051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey1_50051/08_2025/9ey1_50051.map" model { file = "/net/cci-nas-00/data/ceres_data/9ey1_50051/08_2025/9ey1_50051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey1_50051/08_2025/9ey1_50051.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 1 6.06 5 P 72 5.49 5 S 86 5.16 5 C 10336 2.51 5 N 2949 2.21 5 O 3325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16769 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 5512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5512 Classifications: {'peptide': 705} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 660} Chain breaks: 2 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: "T" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1461 Classifications: {'RNA': 69} Modifications used: {'rna2p': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 25, 'rna3p_pyr': 27} Link IDs: {'rna2p': 17, 'rna3p': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2345 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.26 Number of scatterers: 16769 At special positions: 0 Unit cell: (106.05, 117.16, 172.71, 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 1 29.99 S 86 16.00 P 72 15.00 O 3325 8.00 N 2949 7.00 C 10336 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=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 757.8 milliseconds Enol-peptide restraints added in 1.9 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" NE2 HIS E 551 " pdb="ZN ZN E1000 " - pdb=" NE2 HIS E 724 " 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3662 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 15 sheets defined 49.5% alpha, 13.6% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'E' and resid 37 through 42 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 152 removed outlier: 3.500A pdb=" N GLU E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 263 removed outlier: 3.829A pdb=" N LYS E 260 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 281 removed outlier: 4.171A pdb=" N ALA E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 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: 3.685A pdb=" N GLN E 327 " --> pdb=" O ASN E 323 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY E 331 " --> pdb=" O GLN E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 351 removed outlier: 3.568A pdb=" N LEU E 349 " --> pdb=" O PRO E 345 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP E 351 " --> pdb=" O SER E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 362 removed outlier: 3.637A pdb=" N TRP E 357 " --> pdb=" O ARG E 353 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET E 358 " --> pdb=" O TYR E 354 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 361 " --> pdb=" O TRP E 357 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY E 362 " --> pdb=" O MET E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 393 removed outlier: 4.024A pdb=" N ILE E 392 " --> pdb=" O GLN E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 removed outlier: 4.001A 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 552 Processing helix chain 'E' and resid 554 through 570 Processing helix chain 'E' and resid 583 through 595 removed outlier: 4.094A 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 608 through 611 Processing helix chain 'E' and resid 618 through 632 removed outlier: 3.818A pdb=" N LEU E 624 " --> pdb=" O ALA E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 677 Processing helix chain 'E' and resid 693 through 700 Processing helix chain 'E' and resid 704 through 716 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 763 removed outlier: 4.006A pdb=" N LYS E 762 " --> pdb=" O PRO E 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 771 removed outlier: 3.513A pdb=" N LYS E 768 " --> pdb=" O ILE E 764 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 769 " --> pdb=" O PRO E 765 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 791 removed outlier: 3.770A pdb=" N GLU E 777 " --> pdb=" O GLY E 773 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU E 786 " --> pdb=" O ARG E 782 " (cutoff:3.500A) 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 54 removed outlier: 3.838A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 122 removed outlier: 3.546A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.519A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.516A 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 221 removed outlier: 3.628A pdb=" N VAL A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.676A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.608A 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 54 removed outlier: 3.632A 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 Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.826A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 186 removed outlier: 4.597A 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 210 through 221 removed outlier: 3.618A 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 34 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 121 Processing helix chain 'C' and resid 121 through 137 removed outlier: 3.864A pdb=" N GLY C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.770A 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: 3.629A pdb=" N PHE C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.518A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 33 removed outlier: 3.556A pdb=" N LEU D 24 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.733A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 137 removed outlier: 3.679A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 165 through 186 removed outlier: 4.729A 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 204 through 209 removed outlier: 4.069A pdb=" N LEU D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 removed outlier: 3.720A pdb=" N SER D 219 " --> pdb=" O ASN D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.502A pdb=" N TYR D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 105 removed outlier: 4.116A pdb=" N ILE F 98 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N MET F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY F 105 " --> pdb=" O TRP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.539A pdb=" N MET F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS F 123 " --> pdb=" O THR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 164 removed outlier: 3.986A pdb=" N GLU F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.667A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 removed outlier: 3.543A 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: 3.708A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 269 " --> pdb=" O TRP F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 282 Processing helix chain 'F' and resid 320 through 329 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 'E' and resid 162 through 167 removed outlier: 6.682A pdb=" N CYS E 136 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ARG E 166 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU E 138 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP E 106 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER E 139 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE E 108 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG E 82 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE E 109 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU E 84 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA E 73 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 63 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL E 58 " --> pdb=" O LEU E 427 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.584A pdb=" N TYR E 173 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA E 305 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL E 340 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL E 307 " --> pdb=" O VAL E 340 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS E 342 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL E 309 " --> pdb=" O HIS E 342 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS E 367 " --> pdb=" O VAL E 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.540A pdb=" N ILE E 291 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS E 286 " --> pdb=" O ARG E 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 602 through 606 removed outlier: 5.907A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA E 540 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL E 579 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 542 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N SER E 511 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL E 542 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU E 513 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR E 510 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET E 750 " --> pdb=" O PHE E 485 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 634 through 638 removed outlier: 6.331A pdb=" N LEU E 683 " --> pdb=" O MET E 721 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ASN E 723 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS E 685 " --> pdb=" O ASN E 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.720A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA A 13 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A 40 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 15 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.585A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.563A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB3, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.582A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU D 253 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA D 197 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB5, first strand: chain 'F' and resid 272 through 273 removed outlier: 6.441A pdb=" N LEU F 205 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N CYS F 246 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE F 207 " --> pdb=" O CYS F 246 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.810A 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: 6.031A pdb=" N GLN F 343 " --> pdb=" O THR F 382 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4724 1.33 - 1.45: 2999 1.45 - 1.57: 9217 1.57 - 1.69: 142 1.69 - 1.82: 136 Bond restraints: 17218 Sorted by residual: bond pdb=" C2 1MA T 9 " pdb=" N3 1MA T 9 " ideal model delta sigma weight residual 1.290 1.458 -0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N3 1MA T 9 " pdb=" C4 1MA T 9 " ideal model delta sigma weight residual 1.353 1.515 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" C5 1MA T 9 " pdb=" C6 1MA T 9 " ideal model delta sigma weight residual 1.437 1.533 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" N1 1MA T 9 " pdb=" C2 1MA T 9 " ideal model delta sigma weight residual 1.359 1.435 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" N HIS E 546 " pdb=" CA HIS E 546 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.29e-02 6.01e+03 8.20e+00 ... (remaining 17213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.86: 23626 6.86 - 13.72: 26 13.72 - 20.58: 1 20.58 - 27.44: 0 27.44 - 34.30: 2 Bond angle restraints: 23655 Sorted by residual: angle pdb=" C1' 1MA T 9 " pdb=" N9 1MA T 9 " pdb=" C8 1MA T 9 " ideal model delta sigma weight residual 127.61 93.31 34.30 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C1' 1MA T 9 " pdb=" N9 1MA T 9 " pdb=" C4 1MA T 9 " ideal model delta sigma weight residual 125.83 158.95 -33.12 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CA HIS E 702 " pdb=" C HIS E 702 " pdb=" O HIS E 702 " ideal model delta sigma weight residual 120.89 114.52 6.37 1.10e+00 8.26e-01 3.36e+01 angle pdb=" C GLY E 160 " pdb=" N ILE E 161 " pdb=" CA ILE E 161 " ideal model delta sigma weight residual 123.14 116.98 6.16 1.31e+00 5.83e-01 2.21e+01 angle pdb=" PA GTP T 201 " pdb=" O3A GTP T 201 " pdb=" PB GTP T 201 " ideal model delta sigma weight residual 120.50 134.53 -14.03 3.00e+00 1.11e-01 2.19e+01 ... (remaining 23650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 9954 34.82 - 69.64: 462 69.64 - 104.46: 60 104.46 - 139.28: 6 139.28 - 174.10: 1 Dihedral angle restraints: 10483 sinusoidal: 4784 harmonic: 5699 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 232.00 57.90 174.10 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O3B GTP T 201 " pdb=" O3A GTP T 201 " pdb=" PB GTP T 201 " pdb=" PA GTP T 201 " ideal model delta sinusoidal sigma weight residual -68.92 59.04 -127.96 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" O2G GTP T 201 " pdb=" O3B GTP T 201 " pdb=" PG GTP T 201 " pdb=" PB GTP T 201 " ideal model delta sinusoidal sigma weight residual 177.30 -58.66 -124.04 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 10480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2716 0.113 - 0.227: 46 0.227 - 0.340: 1 0.340 - 0.454: 2 0.454 - 0.567: 3 Chirality restraints: 2768 Sorted by residual: chirality pdb=" P U T 2 " pdb=" OP1 U T 2 " pdb=" OP2 U T 2 " pdb=" O5' U T 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" P A T 67 " pdb=" OP1 A T 67 " pdb=" OP2 A T 67 " pdb=" O5' A T 67 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" P C T 68 " pdb=" OP1 C T 68 " pdb=" OP2 C T 68 " pdb=" O5' C T 68 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 2765 not shown) Planarity restraints: 2821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 187 " -0.038 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO A 188 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 229 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO C 230 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 229 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO B 230 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " 0.026 5.00e-02 4.00e+02 ... (remaining 2818 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 207 2.63 - 3.20: 15174 3.20 - 3.77: 27790 3.77 - 4.33: 39327 4.33 - 4.90: 61678 Nonbonded interactions: 144176 Sorted by model distance: nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E1000 " model vdw 2.066 2.230 nonbonded pdb=" OD2 ASP E 550 " pdb="ZN ZN E1000 " model vdw 2.067 2.230 nonbonded pdb=" O2' 1MA T 9 " pdb=" OD1 ASN F 222 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR C 153 " pdb=" OH TYR C 233 " model vdw 2.209 3.040 nonbonded pdb=" O LEU F 290 " pdb=" O2' SAH F 501 " model vdw 2.226 3.040 ... (remaining 144171 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: 5.920 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.240 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 0.444 17220 Z= 0.270 Angle : 0.809 34.298 23655 Z= 0.411 Chirality : 0.047 0.567 2768 Planarity : 0.005 0.058 2821 Dihedral : 18.770 174.103 6821 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 1.66 % Allowed : 20.96 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.19), residues: 1991 helix: 0.68 (0.18), residues: 817 sheet: -0.18 (0.28), residues: 359 loop : 0.11 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 785 TYR 0.028 0.001 TYR F 132 PHE 0.014 0.001 PHE F 384 TRP 0.019 0.001 TRP E 433 HIS 0.009 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00447 (17218) covalent geometry : angle 0.80863 (23655) hydrogen bonds : bond 0.23833 ( 751) hydrogen bonds : angle 8.32075 ( 2112) metal coordination : bond 0.31387 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 374 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: E 138 LEU cc_start: 0.7760 (mp) cc_final: 0.7524 (mm) REVERT: E 145 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7497 (mp0) REVERT: E 181 TYR cc_start: 0.8073 (m-80) cc_final: 0.7760 (m-10) REVERT: E 249 LEU cc_start: 0.8721 (tt) cc_final: 0.8057 (mt) REVERT: E 306 PHE cc_start: 0.7928 (p90) cc_final: 0.7641 (p90) REVERT: E 309 VAL cc_start: 0.8136 (p) cc_final: 0.7859 (m) REVERT: E 310 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: E 436 ASP cc_start: 0.7968 (t0) cc_final: 0.7752 (m-30) REVERT: E 449 GLU cc_start: 0.8889 (tp30) cc_final: 0.8617 (tp30) REVERT: E 490 SER cc_start: 0.7431 (p) cc_final: 0.7206 (m) REVERT: E 524 LEU cc_start: 0.8429 (mt) cc_final: 0.8044 (mt) REVERT: E 546 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6398 (p-80) REVERT: E 588 LEU cc_start: 0.8009 (mm) cc_final: 0.7740 (mt) REVERT: E 602 ILE cc_start: 0.7915 (mm) cc_final: 0.7707 (tp) REVERT: E 682 LEU cc_start: 0.8383 (tp) cc_final: 0.8146 (tm) REVERT: E 716 ASN cc_start: 0.7938 (t0) cc_final: 0.7727 (t0) REVERT: E 760 MET cc_start: 0.7924 (mmm) cc_final: 0.7723 (mmm) REVERT: E 777 GLU cc_start: 0.8516 (tt0) cc_final: 0.8086 (tm-30) REVERT: A 28 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6496 (tt0) REVERT: A 70 ASP cc_start: 0.6734 (m-30) cc_final: 0.6137 (m-30) REVERT: A 84 ARG cc_start: 0.7312 (ptm160) cc_final: 0.7008 (ptm160) REVERT: A 105 LYS cc_start: 0.6962 (mtmt) cc_final: 0.6373 (mttm) REVERT: A 118 LEU cc_start: 0.6634 (mp) cc_final: 0.6401 (mm) REVERT: A 123 MET cc_start: 0.7130 (ttp) cc_final: 0.6646 (tmm) REVERT: A 135 GLU cc_start: 0.6445 (mm-30) cc_final: 0.6095 (mp0) REVERT: A 160 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: A 162 GLN cc_start: 0.6793 (mt0) cc_final: 0.6341 (mt0) REVERT: A 211 GLU cc_start: 0.6200 (pm20) cc_final: 0.5765 (pm20) REVERT: A 236 LEU cc_start: 0.7279 (tp) cc_final: 0.6930 (tp) REVERT: A 242 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6598 (mt-10) REVERT: B 30 LEU cc_start: 0.6208 (mt) cc_final: 0.5886 (mm) REVERT: B 41 ASP cc_start: 0.6711 (t0) cc_final: 0.6496 (t0) REVERT: B 44 ASN cc_start: 0.7233 (p0) cc_final: 0.6867 (p0) REVERT: B 48 GLU cc_start: 0.6991 (tp30) cc_final: 0.6529 (tp30) REVERT: B 52 LYS cc_start: 0.7137 (mtpt) cc_final: 0.6721 (mtpp) REVERT: B 69 LYS cc_start: 0.6733 (tptp) cc_final: 0.6445 (ttmm) REVERT: B 70 ASP cc_start: 0.6455 (m-30) cc_final: 0.6026 (m-30) REVERT: B 79 LYS cc_start: 0.6705 (tptt) cc_final: 0.6223 (ttmm) REVERT: B 96 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6582 (p) REVERT: B 99 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6849 (mtpp) REVERT: B 112 GLU cc_start: 0.6842 (mp0) cc_final: 0.6331 (mm-30) REVERT: B 140 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6929 (tp30) REVERT: B 143 GLN cc_start: 0.6587 (pm20) cc_final: 0.6005 (mp10) REVERT: B 159 PHE cc_start: 0.5220 (m-80) cc_final: 0.4308 (t80) REVERT: B 160 GLU cc_start: 0.6037 (mp0) cc_final: 0.5570 (mt-10) REVERT: B 162 GLN cc_start: 0.6799 (mt0) cc_final: 0.6497 (mt0) REVERT: B 194 MET cc_start: 0.6670 (mmm) cc_final: 0.6453 (mmm) REVERT: B 242 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6433 (mp0) REVERT: B 257 ILE cc_start: 0.7463 (tt) cc_final: 0.7181 (tp) REVERT: B 260 GLN cc_start: 0.7534 (mm110) cc_final: 0.7289 (tp40) REVERT: C 41 ASP cc_start: 0.7104 (t0) cc_final: 0.6896 (t70) REVERT: C 48 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6991 (tp30) REVERT: C 52 LYS cc_start: 0.7337 (tppt) cc_final: 0.7084 (tppt) REVERT: C 53 LYS cc_start: 0.7429 (ttpp) cc_final: 0.6902 (ttpp) REVERT: C 69 LYS cc_start: 0.8271 (tppt) cc_final: 0.7390 (mtmm) REVERT: C 104 LYS cc_start: 0.7308 (tttt) cc_final: 0.7042 (ttmt) REVERT: C 107 GLN cc_start: 0.6390 (tt0) cc_final: 0.6033 (mt0) REVERT: C 112 GLU cc_start: 0.6745 (mp0) cc_final: 0.6531 (mp0) REVERT: C 120 VAL cc_start: 0.7247 (t) cc_final: 0.7039 (t) REVERT: C 135 GLU cc_start: 0.6540 (tp30) cc_final: 0.6297 (mm-30) REVERT: C 189 ILE cc_start: 0.6778 (mt) cc_final: 0.6556 (mt) REVERT: C 212 LYS cc_start: 0.7284 (mtmm) cc_final: 0.6953 (mttt) REVERT: C 242 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6431 (mt-10) REVERT: C 251 ILE cc_start: 0.7919 (mt) cc_final: 0.7711 (mm) REVERT: C 259 MET cc_start: 0.6775 (mmm) cc_final: 0.6471 (mmm) REVERT: D 24 LEU cc_start: 0.7243 (tp) cc_final: 0.7018 (tp) REVERT: D 48 GLU cc_start: 0.6550 (pm20) cc_final: 0.6187 (mp0) REVERT: D 56 ASN cc_start: 0.7576 (p0) cc_final: 0.7312 (p0) REVERT: D 79 LYS cc_start: 0.6797 (mmmm) cc_final: 0.6229 (tppt) REVERT: D 81 LYS cc_start: 0.7273 (tmtm) cc_final: 0.6939 (tmtt) REVERT: D 84 ARG cc_start: 0.6854 (ptm-80) cc_final: 0.6466 (ptp-110) REVERT: D 86 ASP cc_start: 0.6642 (m-30) cc_final: 0.6330 (m-30) REVERT: D 123 MET cc_start: 0.6644 (tmm) cc_final: 0.6150 (tmm) REVERT: D 138 GLN cc_start: 0.7611 (mm110) cc_final: 0.7408 (mm-40) REVERT: D 159 PHE cc_start: 0.6043 (m-80) cc_final: 0.5362 (m-80) REVERT: D 179 THR cc_start: 0.6332 (t) cc_final: 0.6113 (m) REVERT: D 194 MET cc_start: 0.7302 (mmm) cc_final: 0.6836 (mmm) REVERT: D 205 LEU cc_start: 0.5786 (tp) cc_final: 0.5332 (mt) REVERT: D 226 ARG cc_start: 0.6729 (ptt90) cc_final: 0.5713 (ppt170) REVERT: D 232 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5918 (mt-10) REVERT: F 116 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7855 (mt-10) REVERT: F 130 LYS cc_start: 0.8160 (tttt) cc_final: 0.7550 (tttm) REVERT: F 178 LEU cc_start: 0.7449 (tp) cc_final: 0.7247 (tp) REVERT: F 191 MET cc_start: 0.7251 (mtm) cc_final: 0.6984 (mtp) REVERT: F 209 MET cc_start: 0.7609 (mmt) cc_final: 0.7033 (mmt) REVERT: F 214 TYR cc_start: 0.7170 (m-80) cc_final: 0.6725 (m-10) REVERT: F 250 ILE cc_start: 0.7028 (mt) cc_final: 0.6609 (tp) REVERT: F 276 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7796 (mppt) REVERT: F 327 LYS cc_start: 0.7880 (mttm) cc_final: 0.7656 (mmpt) REVERT: F 336 LEU cc_start: 0.7561 (mt) cc_final: 0.7361 (mt) REVERT: F 356 MET cc_start: 0.7626 (mmm) cc_final: 0.7238 (mmm) REVERT: F 360 LEU cc_start: 0.7882 (mt) cc_final: 0.7659 (mt) outliers start: 27 outliers final: 13 residues processed: 398 average time/residue: 0.5613 time to fit residues: 247.4892 Evaluate side-chains 259 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 702 HIS Chi-restraints excluded: chain E residue 703 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 132 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 455 ASN B 107 GLN C 162 GLN D 102 ASN D 143 GLN F 200 GLN F 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.117047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.087408 restraints weight = 29542.368| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.29 r_work: 0.3082 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17220 Z= 0.171 Angle : 0.664 7.809 23655 Z= 0.335 Chirality : 0.044 0.159 2768 Planarity : 0.005 0.052 2821 Dihedral : 15.587 177.524 3218 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.49 % Allowed : 20.41 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.19), residues: 1991 helix: 1.00 (0.18), residues: 853 sheet: -0.33 (0.26), residues: 348 loop : -0.05 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 43 TYR 0.018 0.002 TYR E 729 PHE 0.017 0.002 PHE E 521 TRP 0.012 0.002 TRP F 183 HIS 0.005 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00378 (17218) covalent geometry : angle 0.66415 (23655) hydrogen bonds : bond 0.05310 ( 751) hydrogen bonds : angle 5.60829 ( 2112) metal coordination : bond 0.01086 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 245 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8523 (tt) cc_final: 0.7910 (mt) REVERT: E 262 MET cc_start: 0.8521 (mmm) cc_final: 0.8316 (mpm) REVERT: E 479 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6724 (tm130) REVERT: E 524 LEU cc_start: 0.8140 (mt) cc_final: 0.7914 (mt) REVERT: E 588 LEU cc_start: 0.7698 (mm) cc_final: 0.7406 (mt) REVERT: E 715 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5306 (mtp) REVERT: E 720 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7821 (mp) REVERT: E 760 MET cc_start: 0.7800 (mmm) cc_final: 0.7314 (mmm) REVERT: E 778 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6870 (mtp) REVERT: A 28 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6854 (tt0) REVERT: A 40 LEU cc_start: 0.7766 (tt) cc_final: 0.7501 (tm) REVERT: A 102 ASN cc_start: 0.7824 (t0) cc_final: 0.7463 (t0) REVERT: A 112 GLU cc_start: 0.6739 (mp0) cc_final: 0.6311 (mm-30) REVERT: A 140 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7199 (tp30) REVERT: A 213 VAL cc_start: 0.7619 (t) cc_final: 0.7409 (t) REVERT: A 232 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6704 (mp0) REVERT: A 242 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6666 (mt-10) REVERT: B 48 GLU cc_start: 0.7426 (tp30) cc_final: 0.7122 (tp30) REVERT: B 52 LYS cc_start: 0.7363 (mtpt) cc_final: 0.7154 (mtpp) REVERT: B 143 GLN cc_start: 0.6513 (pm20) cc_final: 0.6226 (mp10) REVERT: C 53 LYS cc_start: 0.7949 (ttpp) cc_final: 0.7708 (ttpt) REVERT: C 69 LYS cc_start: 0.7828 (tppt) cc_final: 0.7513 (mtmm) REVERT: C 118 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7056 (mp) REVERT: C 120 VAL cc_start: 0.7092 (t) cc_final: 0.6883 (t) REVERT: C 147 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7748 (mtt90) REVERT: C 159 PHE cc_start: 0.7337 (m-80) cc_final: 0.7130 (m-80) REVERT: C 189 ILE cc_start: 0.7387 (mt) cc_final: 0.7072 (mt) REVERT: C 212 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7317 (mttt) REVERT: D 48 GLU cc_start: 0.6698 (pm20) cc_final: 0.6359 (mp0) REVERT: D 56 ASN cc_start: 0.7690 (p0) cc_final: 0.7456 (p0) REVERT: D 81 LYS cc_start: 0.7295 (tmtm) cc_final: 0.7084 (tmtt) REVERT: D 84 ARG cc_start: 0.7067 (ptm-80) cc_final: 0.6639 (ptp90) REVERT: D 110 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7440 (p) REVERT: D 123 MET cc_start: 0.7246 (tmm) cc_final: 0.6927 (tmm) REVERT: D 236 LEU cc_start: 0.7776 (tp) cc_final: 0.7546 (tp) REVERT: D 260 GLN cc_start: 0.6135 (OUTLIER) cc_final: 0.5593 (pm20) REVERT: F 104 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8249 (tm) REVERT: F 120 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8562 (mt) REVERT: F 130 LYS cc_start: 0.8055 (tttt) cc_final: 0.7722 (mttt) REVERT: F 191 MET cc_start: 0.7290 (mtm) cc_final: 0.6944 (mtp) REVERT: F 209 MET cc_start: 0.7585 (mmt) cc_final: 0.7161 (mmt) REVERT: F 214 TYR cc_start: 0.7196 (m-80) cc_final: 0.6769 (m-10) REVERT: F 221 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6683 (tp40) REVERT: F 276 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7801 (mppt) outliers start: 73 outliers final: 21 residues processed: 298 average time/residue: 0.5039 time to fit residues: 168.7849 Evaluate side-chains 226 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 623 ARG Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 727 GLN Chi-restraints excluded: chain E residue 778 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 67 optimal weight: 0.0570 chunk 114 optimal weight: 0.0770 chunk 190 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 461 GLN B 107 GLN D 102 ASN F 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089957 restraints weight = 30102.880| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.26 r_work: 0.3117 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17220 Z= 0.123 Angle : 0.587 9.272 23655 Z= 0.293 Chirality : 0.042 0.263 2768 Planarity : 0.005 0.050 2821 Dihedral : 15.216 177.102 3193 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.24 % Allowed : 21.20 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 1991 helix: 1.27 (0.18), residues: 854 sheet: -0.32 (0.26), residues: 341 loop : -0.24 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 785 TYR 0.017 0.001 TYR F 137 PHE 0.019 0.001 PHE D 159 TRP 0.009 0.001 TRP F 183 HIS 0.005 0.001 HIS E 552 Details of bonding type rmsd covalent geometry : bond 0.00271 (17218) covalent geometry : angle 0.58666 (23655) hydrogen bonds : bond 0.04389 ( 751) hydrogen bonds : angle 5.17907 ( 2112) metal coordination : bond 0.00168 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: E 95 MET cc_start: 0.7802 (ttm) cc_final: 0.7574 (ttm) REVERT: E 249 LEU cc_start: 0.8547 (tt) cc_final: 0.7919 (mt) REVERT: E 262 MET cc_start: 0.8509 (mmm) cc_final: 0.8237 (mpm) REVERT: E 479 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6660 (tm130) REVERT: E 524 LEU cc_start: 0.8224 (mt) cc_final: 0.8023 (mt) REVERT: E 588 LEU cc_start: 0.7661 (mm) cc_final: 0.7364 (mt) REVERT: E 760 MET cc_start: 0.7844 (mmm) cc_final: 0.7393 (mmm) REVERT: E 778 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6909 (mtp) REVERT: A 28 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6925 (tt0) REVERT: A 40 LEU cc_start: 0.7786 (tt) cc_final: 0.7542 (tm) REVERT: A 70 ASP cc_start: 0.7188 (m-30) cc_final: 0.6754 (m-30) REVERT: A 102 ASN cc_start: 0.7687 (t0) cc_final: 0.7397 (t0) REVERT: A 112 GLU cc_start: 0.6753 (mp0) cc_final: 0.6348 (mm-30) REVERT: A 123 MET cc_start: 0.7148 (tmm) cc_final: 0.6914 (tmm) REVERT: A 140 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7156 (tp30) REVERT: A 232 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6683 (mp0) REVERT: A 242 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6553 (mt-10) REVERT: B 52 LYS cc_start: 0.7384 (mtpt) cc_final: 0.7162 (mtpp) REVERT: B 79 LYS cc_start: 0.7215 (tptt) cc_final: 0.6547 (ttmm) REVERT: B 104 LYS cc_start: 0.7447 (mtmm) cc_final: 0.6740 (mmmm) REVERT: B 143 GLN cc_start: 0.6561 (pm20) cc_final: 0.6300 (mp10) REVERT: B 226 ARG cc_start: 0.7215 (ptt90) cc_final: 0.6993 (ptm-80) REVERT: B 242 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: C 69 LYS cc_start: 0.7755 (tppt) cc_final: 0.7443 (mtmm) REVERT: C 147 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7770 (mtt90) REVERT: D 48 GLU cc_start: 0.6530 (pm20) cc_final: 0.6288 (mp0) REVERT: D 81 LYS cc_start: 0.7270 (tmtm) cc_final: 0.6986 (mmmm) REVERT: D 84 ARG cc_start: 0.6910 (ptm-80) cc_final: 0.6490 (ptp90) REVERT: D 110 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7331 (p) REVERT: D 123 MET cc_start: 0.7301 (tmm) cc_final: 0.6991 (tmm) REVERT: D 143 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6825 (pm20) REVERT: D 236 LEU cc_start: 0.7713 (tp) cc_final: 0.7451 (tp) REVERT: F 104 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8252 (tm) REVERT: F 130 LYS cc_start: 0.8078 (tttt) cc_final: 0.7601 (tttm) REVERT: F 144 LYS cc_start: 0.8286 (mmmm) cc_final: 0.7689 (mmtm) REVERT: F 191 MET cc_start: 0.7237 (mtm) cc_final: 0.6998 (mtp) REVERT: F 209 MET cc_start: 0.7561 (mmt) cc_final: 0.7060 (mmt) REVERT: F 214 TYR cc_start: 0.7224 (m-80) cc_final: 0.6814 (m-10) REVERT: F 330 ASN cc_start: 0.6667 (m-40) cc_final: 0.6312 (m-40) outliers start: 69 outliers final: 24 residues processed: 268 average time/residue: 0.5368 time to fit residues: 160.2191 Evaluate side-chains 221 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 778 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 86 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 91 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 390 ASN E 505 ASN B 107 GLN C 44 ASN C 220 GLN D 56 ASN F 162 ASN F 221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089775 restraints weight = 29637.337| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.33 r_work: 0.3112 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17220 Z= 0.132 Angle : 0.592 8.004 23655 Z= 0.295 Chirality : 0.042 0.155 2768 Planarity : 0.005 0.048 2821 Dihedral : 15.020 177.805 3191 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.24 % Allowed : 21.76 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.19), residues: 1991 helix: 1.34 (0.18), residues: 853 sheet: -0.45 (0.26), residues: 335 loop : -0.31 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 526 TYR 0.020 0.002 TYR F 137 PHE 0.024 0.002 PHE E 306 TRP 0.009 0.001 TRP E 587 HIS 0.004 0.001 HIS E 552 Details of bonding type rmsd covalent geometry : bond 0.00296 (17218) covalent geometry : angle 0.59245 (23655) hydrogen bonds : bond 0.04213 ( 751) hydrogen bonds : angle 5.03003 ( 2112) metal coordination : bond 0.00118 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 0.426 Fit side-chains REVERT: E 95 MET cc_start: 0.7847 (ttm) cc_final: 0.7583 (ttm) REVERT: E 249 LEU cc_start: 0.8645 (tt) cc_final: 0.8023 (mt) REVERT: E 479 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6662 (tm130) REVERT: E 588 LEU cc_start: 0.7679 (mm) cc_final: 0.7372 (mt) REVERT: E 760 MET cc_start: 0.7820 (mmm) cc_final: 0.7459 (mmm) REVERT: A 28 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7018 (tt0) REVERT: A 40 LEU cc_start: 0.7747 (tt) cc_final: 0.7499 (tm) REVERT: A 52 LYS cc_start: 0.7306 (tmmt) cc_final: 0.7057 (tmmt) REVERT: A 69 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6762 (ttpp) REVERT: A 70 ASP cc_start: 0.7288 (m-30) cc_final: 0.6872 (m-30) REVERT: A 102 ASN cc_start: 0.7815 (t0) cc_final: 0.7559 (t0) REVERT: A 112 GLU cc_start: 0.6857 (mp0) cc_final: 0.6492 (mm-30) REVERT: A 123 MET cc_start: 0.7445 (tmm) cc_final: 0.7179 (tmm) REVERT: A 140 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7147 (tp30) REVERT: A 232 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6780 (mp0) REVERT: A 242 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6617 (mt-10) REVERT: B 52 LYS cc_start: 0.7364 (mtpt) cc_final: 0.7146 (mtpp) REVERT: B 79 LYS cc_start: 0.7207 (tptt) cc_final: 0.6627 (ttmm) REVERT: B 104 LYS cc_start: 0.7421 (mtmm) cc_final: 0.6756 (mmmm) REVERT: B 111 LEU cc_start: 0.7280 (tp) cc_final: 0.6998 (tp) REVERT: B 142 ASP cc_start: 0.6214 (p0) cc_final: 0.5843 (p0) REVERT: B 143 GLN cc_start: 0.6542 (pm20) cc_final: 0.6284 (mp10) REVERT: B 226 ARG cc_start: 0.7248 (ptt90) cc_final: 0.6991 (ptm-80) REVERT: C 69 LYS cc_start: 0.7820 (tppt) cc_final: 0.7484 (mtmm) REVERT: C 118 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7102 (mp) REVERT: C 147 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7737 (mtt90) REVERT: C 189 ILE cc_start: 0.7466 (mt) cc_final: 0.7160 (mt) REVERT: D 81 LYS cc_start: 0.7210 (tmtm) cc_final: 0.6925 (mmmm) REVERT: D 123 MET cc_start: 0.7321 (tmm) cc_final: 0.7053 (tmm) REVERT: D 143 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: D 236 LEU cc_start: 0.7669 (tp) cc_final: 0.7423 (tp) REVERT: D 260 GLN cc_start: 0.6178 (OUTLIER) cc_final: 0.5692 (pm20) REVERT: F 130 LYS cc_start: 0.8083 (tttt) cc_final: 0.7601 (tttm) REVERT: F 144 LYS cc_start: 0.8298 (mmmm) cc_final: 0.7621 (mmtm) REVERT: F 148 ILE cc_start: 0.8597 (mp) cc_final: 0.8295 (pp) REVERT: F 191 MET cc_start: 0.7189 (mtm) cc_final: 0.6907 (mtp) REVERT: F 209 MET cc_start: 0.7597 (mmt) cc_final: 0.7167 (mmt) REVERT: F 214 TYR cc_start: 0.7251 (m-80) cc_final: 0.6827 (m-10) REVERT: F 330 ASN cc_start: 0.6641 (m-40) cc_final: 0.6278 (m-40) outliers start: 69 outliers final: 32 residues processed: 257 average time/residue: 0.5230 time to fit residues: 151.1589 Evaluate side-chains 225 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 61 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 379 ASN ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN C 44 ASN D 56 ASN F 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.117373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.087208 restraints weight = 29624.528| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.29 r_work: 0.3088 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17220 Z= 0.267 Angle : 0.753 9.358 23655 Z= 0.381 Chirality : 0.048 0.218 2768 Planarity : 0.006 0.051 2821 Dihedral : 15.273 178.137 3191 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.10 % Allowed : 21.08 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.18), residues: 1991 helix: 0.77 (0.17), residues: 851 sheet: -0.81 (0.26), residues: 325 loop : -0.58 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 623 TYR 0.023 0.003 TYR F 137 PHE 0.021 0.003 PHE A 223 TRP 0.016 0.003 TRP F 101 HIS 0.009 0.002 HIS F 278 Details of bonding type rmsd covalent geometry : bond 0.00618 (17218) covalent geometry : angle 0.75278 (23655) hydrogen bonds : bond 0.05665 ( 751) hydrogen bonds : angle 5.49244 ( 2112) metal coordination : bond 0.00424 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 200 time to evaluate : 0.558 Fit side-chains REVERT: E 79 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: E 95 MET cc_start: 0.7739 (ttm) cc_final: 0.7430 (ttm) REVERT: E 99 LYS cc_start: 0.8440 (tppt) cc_final: 0.8181 (tppt) REVERT: E 249 LEU cc_start: 0.8666 (tt) cc_final: 0.8085 (mt) REVERT: E 262 MET cc_start: 0.8380 (mmm) cc_final: 0.7905 (mpm) REVERT: E 416 MET cc_start: 0.7436 (pp-130) cc_final: 0.7228 (pp-130) REVERT: E 479 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6619 (tm130) REVERT: E 587 TRP cc_start: 0.6821 (t60) cc_final: 0.6536 (t60) REVERT: E 610 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7369 (mm) REVERT: E 715 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5408 (mtp) REVERT: E 720 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7839 (mp) REVERT: E 760 MET cc_start: 0.7969 (mmm) cc_final: 0.7533 (mmm) REVERT: E 778 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7265 (mtt) REVERT: E 780 GLU cc_start: 0.8556 (pp20) cc_final: 0.8311 (pp20) REVERT: A 64 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6788 (t0) REVERT: A 69 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6796 (ttpp) REVERT: A 102 ASN cc_start: 0.7844 (t0) cc_final: 0.7527 (t0) REVERT: A 232 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6964 (mp0) REVERT: A 241 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7849 (mp) REVERT: B 112 GLU cc_start: 0.7472 (mp0) cc_final: 0.6998 (mp0) REVERT: B 142 ASP cc_start: 0.6347 (p0) cc_final: 0.5875 (p0) REVERT: B 242 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6766 (mt-10) REVERT: C 69 LYS cc_start: 0.7895 (tppt) cc_final: 0.7578 (mppt) REVERT: C 118 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7030 (mp) REVERT: C 147 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7733 (mtt90) REVERT: D 81 LYS cc_start: 0.7431 (tmtm) cc_final: 0.7217 (tmtt) REVERT: D 110 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7408 (p) REVERT: D 123 MET cc_start: 0.7377 (tmm) cc_final: 0.7112 (tmm) REVERT: D 260 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5703 (pm20) REVERT: F 104 LEU cc_start: 0.8657 (mm) cc_final: 0.8157 (tm) REVERT: F 115 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: F 130 LYS cc_start: 0.8141 (tttt) cc_final: 0.7746 (mttt) REVERT: F 131 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7707 (ttmt) REVERT: F 133 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7750 (mm) REVERT: F 144 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8163 (mmtm) REVERT: F 148 ILE cc_start: 0.8617 (mp) cc_final: 0.8317 (pp) REVERT: F 191 MET cc_start: 0.7299 (mtm) cc_final: 0.7020 (mtp) REVERT: F 209 MET cc_start: 0.7617 (mmt) cc_final: 0.7259 (mmt) REVERT: F 214 TYR cc_start: 0.7248 (m-80) cc_final: 0.6988 (m-80) outliers start: 83 outliers final: 40 residues processed: 262 average time/residue: 0.5431 time to fit residues: 160.4232 Evaluate side-chains 238 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 479 GLN Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain E residue 778 MET Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 2 optimal weight: 0.2980 chunk 130 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN D 56 ASN F 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089486 restraints weight = 29518.729| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.31 r_work: 0.3102 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17220 Z= 0.162 Angle : 0.639 8.516 23655 Z= 0.321 Chirality : 0.043 0.154 2768 Planarity : 0.005 0.050 2821 Dihedral : 15.095 179.940 3191 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.93 % Allowed : 23.60 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.18), residues: 1991 helix: 0.99 (0.18), residues: 861 sheet: -0.90 (0.25), residues: 338 loop : -0.55 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 226 TYR 0.025 0.002 TYR F 137 PHE 0.019 0.002 PHE D 159 TRP 0.012 0.002 TRP E 659 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00371 (17218) covalent geometry : angle 0.63897 (23655) hydrogen bonds : bond 0.04565 ( 751) hydrogen bonds : angle 5.21257 ( 2112) metal coordination : bond 0.00173 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 0.640 Fit side-chains REVERT: E 95 MET cc_start: 0.7820 (ttm) cc_final: 0.7482 (ttm) REVERT: E 99 LYS cc_start: 0.8435 (tppt) cc_final: 0.8187 (tppt) REVERT: E 249 LEU cc_start: 0.8724 (tt) cc_final: 0.8102 (mt) REVERT: E 262 MET cc_start: 0.8475 (mmm) cc_final: 0.8026 (mpm) REVERT: E 610 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7412 (mm) REVERT: E 715 MET cc_start: 0.5807 (OUTLIER) cc_final: 0.5008 (mtp) REVERT: E 720 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7874 (mp) REVERT: E 778 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7222 (mtt) REVERT: A 69 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6731 (ttpp) REVERT: A 70 ASP cc_start: 0.7241 (m-30) cc_final: 0.6777 (m-30) REVERT: A 102 ASN cc_start: 0.7836 (t0) cc_final: 0.7546 (t0) REVERT: A 123 MET cc_start: 0.7480 (tmm) cc_final: 0.7228 (tmm) REVERT: A 185 ASP cc_start: 0.6989 (m-30) cc_final: 0.6680 (t0) REVERT: A 232 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6886 (mp0) REVERT: B 226 ARG cc_start: 0.7409 (ptt90) cc_final: 0.7195 (ptm-80) REVERT: B 242 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6793 (mt-10) REVERT: C 69 LYS cc_start: 0.7912 (tppt) cc_final: 0.7616 (mppt) REVERT: C 118 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7033 (mp) REVERT: C 147 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7707 (mtt90) REVERT: D 81 LYS cc_start: 0.7340 (tmtm) cc_final: 0.7139 (tmtt) REVERT: D 123 MET cc_start: 0.7429 (tmm) cc_final: 0.7172 (tmm) REVERT: D 260 GLN cc_start: 0.6115 (OUTLIER) cc_final: 0.5682 (pm20) REVERT: F 104 LEU cc_start: 0.8710 (mm) cc_final: 0.8285 (tm) REVERT: F 115 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: F 130 LYS cc_start: 0.8137 (tttt) cc_final: 0.7669 (tttm) REVERT: F 144 LYS cc_start: 0.8422 (mmmm) cc_final: 0.7853 (mmtm) REVERT: F 148 ILE cc_start: 0.8587 (mp) cc_final: 0.8310 (pp) REVERT: F 191 MET cc_start: 0.7218 (mtm) cc_final: 0.6932 (mtp) REVERT: F 214 TYR cc_start: 0.7150 (m-80) cc_final: 0.6658 (m-10) outliers start: 64 outliers final: 34 residues processed: 251 average time/residue: 0.5654 time to fit residues: 159.7645 Evaluate side-chains 228 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain E residue 778 MET Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 171 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 611 GLN B 107 GLN D 56 ASN F 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.090422 restraints weight = 29599.611| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.24 r_work: 0.3119 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17220 Z= 0.142 Angle : 0.619 10.174 23655 Z= 0.310 Chirality : 0.043 0.155 2768 Planarity : 0.005 0.051 2821 Dihedral : 14.994 178.997 3191 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.24 % Allowed : 23.48 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.19), residues: 1991 helix: 1.13 (0.18), residues: 861 sheet: -0.90 (0.25), residues: 338 loop : -0.51 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 226 TYR 0.018 0.002 TYR E 729 PHE 0.020 0.002 PHE D 159 TRP 0.014 0.002 TRP F 101 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00324 (17218) covalent geometry : angle 0.61865 (23655) hydrogen bonds : bond 0.04251 ( 751) hydrogen bonds : angle 5.07655 ( 2112) metal coordination : bond 0.00145 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 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: 69 poor density : 193 time to evaluate : 0.634 Fit side-chains REVERT: E 95 MET cc_start: 0.7734 (ttm) cc_final: 0.7384 (ttm) REVERT: E 249 LEU cc_start: 0.8711 (tt) cc_final: 0.8095 (mt) REVERT: E 588 LEU cc_start: 0.7717 (mm) cc_final: 0.7498 (mt) REVERT: E 610 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7447 (mm) REVERT: E 778 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7013 (mtt) REVERT: A 64 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.6600 (t0) REVERT: A 69 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6684 (ttpp) REVERT: A 70 ASP cc_start: 0.7180 (m-30) cc_final: 0.6760 (m-30) REVERT: A 102 ASN cc_start: 0.7793 (t0) cc_final: 0.7516 (t0) REVERT: A 123 MET cc_start: 0.7480 (tmm) cc_final: 0.7207 (tmm) REVERT: A 232 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6849 (mp0) REVERT: B 226 ARG cc_start: 0.7385 (ptt90) cc_final: 0.7142 (ptm-80) REVERT: B 242 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: C 69 LYS cc_start: 0.7895 (tppt) cc_final: 0.7630 (mppt) REVERT: C 118 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7015 (mp) REVERT: C 147 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7763 (mtt90) REVERT: D 123 MET cc_start: 0.7343 (tmm) cc_final: 0.6749 (tmm) REVERT: D 260 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5684 (pm20) REVERT: F 104 LEU cc_start: 0.8725 (mm) cc_final: 0.8334 (tm) REVERT: F 115 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: F 130 LYS cc_start: 0.8205 (tttt) cc_final: 0.7591 (tttm) REVERT: F 144 LYS cc_start: 0.8426 (mmmm) cc_final: 0.7845 (mmtm) REVERT: F 148 ILE cc_start: 0.8596 (mp) cc_final: 0.8314 (pp) REVERT: F 191 MET cc_start: 0.7196 (mtm) cc_final: 0.6898 (mtp) REVERT: F 209 MET cc_start: 0.7568 (mmt) cc_final: 0.7160 (mmt) REVERT: F 214 TYR cc_start: 0.7158 (m-80) cc_final: 0.6666 (m-10) REVERT: F 330 ASN cc_start: 0.6799 (m-40) cc_final: 0.6411 (m-40) outliers start: 69 outliers final: 38 residues processed: 247 average time/residue: 0.4902 time to fit residues: 136.1783 Evaluate side-chains 228 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain E residue 778 MET Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 195 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 186 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 727 GLN A 72 GLN B 107 GLN D 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.118868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090455 restraints weight = 29856.139| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.28 r_work: 0.3125 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17220 Z= 0.161 Angle : 0.652 10.421 23655 Z= 0.324 Chirality : 0.043 0.175 2768 Planarity : 0.005 0.050 2821 Dihedral : 15.014 179.087 3191 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.18 % Allowed : 23.85 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.19), residues: 1991 helix: 1.07 (0.18), residues: 863 sheet: -0.90 (0.25), residues: 338 loop : -0.54 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 226 TYR 0.030 0.002 TYR E 729 PHE 0.019 0.002 PHE D 159 TRP 0.017 0.002 TRP F 101 HIS 0.005 0.001 HIS E 98 Details of bonding type rmsd covalent geometry : bond 0.00371 (17218) covalent geometry : angle 0.65183 (23655) hydrogen bonds : bond 0.04432 ( 751) hydrogen bonds : angle 5.12156 ( 2112) metal coordination : bond 0.00253 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 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: 68 poor density : 181 time to evaluate : 0.621 Fit side-chains REVERT: E 95 MET cc_start: 0.7693 (ttm) cc_final: 0.7333 (ttm) REVERT: E 99 LYS cc_start: 0.8455 (tppt) cc_final: 0.8177 (tppt) REVERT: E 249 LEU cc_start: 0.8696 (tt) cc_final: 0.8065 (mt) REVERT: E 262 MET cc_start: 0.8436 (mmm) cc_final: 0.7822 (mpm) REVERT: E 588 LEU cc_start: 0.7700 (mm) cc_final: 0.7493 (mt) REVERT: A 64 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6671 (t0) REVERT: A 69 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6700 (ttpp) REVERT: A 102 ASN cc_start: 0.7802 (t0) cc_final: 0.7532 (t0) REVERT: A 123 MET cc_start: 0.7445 (tmm) cc_final: 0.7182 (tmm) REVERT: A 232 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6875 (mp0) REVERT: B 226 ARG cc_start: 0.7390 (ptt90) cc_final: 0.7142 (ptm-80) REVERT: B 242 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: C 69 LYS cc_start: 0.7913 (tppt) cc_final: 0.7624 (mppt) REVERT: C 118 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7067 (mp) REVERT: C 147 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7712 (mtt90) REVERT: D 123 MET cc_start: 0.7304 (tmm) cc_final: 0.7024 (tmm) REVERT: D 260 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5734 (pm20) REVERT: F 104 LEU cc_start: 0.8705 (mm) cc_final: 0.8322 (tm) REVERT: F 115 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: F 130 LYS cc_start: 0.8221 (tttt) cc_final: 0.7598 (tttm) REVERT: F 137 TYR cc_start: 0.8212 (t80) cc_final: 0.8010 (t80) REVERT: F 144 LYS cc_start: 0.8388 (mmmm) cc_final: 0.7831 (mmtm) REVERT: F 148 ILE cc_start: 0.8645 (mp) cc_final: 0.8342 (pp) REVERT: F 191 MET cc_start: 0.7193 (mtm) cc_final: 0.6908 (mtp) REVERT: F 209 MET cc_start: 0.7616 (mmt) cc_final: 0.7196 (mmt) REVERT: F 214 TYR cc_start: 0.7228 (m-80) cc_final: 0.6750 (m-10) outliers start: 68 outliers final: 40 residues processed: 237 average time/residue: 0.5108 time to fit residues: 136.2745 Evaluate side-chains 227 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 85 optimal weight: 0.0270 chunk 100 optimal weight: 0.0050 chunk 131 optimal weight: 0.5980 chunk 93 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 overall best weight: 0.2652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 724 HIS E 727 GLN B 107 GLN D 56 ASN F 221 GLN F 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091741 restraints weight = 29869.980| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.24 r_work: 0.3157 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.235 17220 Z= 0.131 Angle : 0.610 9.407 23655 Z= 0.303 Chirality : 0.042 0.165 2768 Planarity : 0.005 0.053 2821 Dihedral : 14.851 177.018 3191 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.40 % Allowed : 25.51 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.19), residues: 1991 helix: 1.33 (0.18), residues: 858 sheet: -0.79 (0.26), residues: 343 loop : -0.40 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 226 TYR 0.030 0.002 TYR E 729 PHE 0.019 0.001 PHE D 159 TRP 0.016 0.002 TRP E 659 HIS 0.003 0.001 HIS E 724 Details of bonding type rmsd covalent geometry : bond 0.00261 (17218) covalent geometry : angle 0.60979 (23655) hydrogen bonds : bond 0.03744 ( 751) hydrogen bonds : angle 4.94784 ( 2112) metal coordination : bond 0.16589 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.671 Fit side-chains REVERT: E 95 MET cc_start: 0.7662 (ttm) cc_final: 0.7334 (ttm) REVERT: E 249 LEU cc_start: 0.8695 (tt) cc_final: 0.8067 (mt) REVERT: E 262 MET cc_start: 0.8452 (mmm) cc_final: 0.7875 (mpm) REVERT: E 504 VAL cc_start: 0.7420 (t) cc_final: 0.7175 (t) REVERT: E 588 LEU cc_start: 0.7711 (mm) cc_final: 0.7505 (mt) REVERT: E 715 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.4708 (mtp) REVERT: E 729 TYR cc_start: 0.4118 (t80) cc_final: 0.3395 (t80) REVERT: E 734 LEU cc_start: 0.6330 (mm) cc_final: 0.6121 (mt) REVERT: E 778 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7612 (mtt) REVERT: A 70 ASP cc_start: 0.7082 (m-30) cc_final: 0.6648 (m-30) REVERT: A 102 ASN cc_start: 0.7744 (t0) cc_final: 0.7534 (t0) REVERT: A 123 MET cc_start: 0.7274 (tmm) cc_final: 0.7048 (tmm) REVERT: A 232 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6883 (mp0) REVERT: B 226 ARG cc_start: 0.7319 (ptt90) cc_final: 0.7103 (ptm-80) REVERT: B 242 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: C 69 LYS cc_start: 0.7868 (tppt) cc_final: 0.7584 (mppt) REVERT: C 118 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7017 (mp) REVERT: C 147 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7731 (mtt90) REVERT: D 123 MET cc_start: 0.7294 (tmm) cc_final: 0.7014 (tmm) REVERT: D 260 GLN cc_start: 0.6203 (OUTLIER) cc_final: 0.5779 (pm20) REVERT: F 104 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8190 (mm) REVERT: F 130 LYS cc_start: 0.8254 (tttt) cc_final: 0.7591 (tttm) REVERT: F 144 LYS cc_start: 0.8298 (mmmm) cc_final: 0.7818 (mmtm) REVERT: F 148 ILE cc_start: 0.8627 (mp) cc_final: 0.8329 (pp) REVERT: F 191 MET cc_start: 0.7177 (mtm) cc_final: 0.6930 (mtp) REVERT: F 209 MET cc_start: 0.7559 (mmt) cc_final: 0.7152 (mmt) REVERT: F 214 TYR cc_start: 0.7146 (m-80) cc_final: 0.6698 (m-10) REVERT: F 330 ASN cc_start: 0.6608 (m-40) cc_final: 0.6225 (m-40) outliers start: 39 outliers final: 18 residues processed: 226 average time/residue: 0.5795 time to fit residues: 147.3371 Evaluate side-chains 206 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 778 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 182 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 GLN E 727 GLN B 107 GLN D 56 ASN F 221 GLN F 242 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.118847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090400 restraints weight = 29565.559| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.24 r_work: 0.3124 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17220 Z= 0.179 Angle : 0.678 10.735 23655 Z= 0.337 Chirality : 0.044 0.156 2768 Planarity : 0.005 0.058 2821 Dihedral : 14.943 179.047 3190 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.58 % Allowed : 26.06 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.19), residues: 1991 helix: 1.06 (0.18), residues: 862 sheet: -0.82 (0.25), residues: 353 loop : -0.47 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 431 TYR 0.034 0.002 TYR E 729 PHE 0.020 0.002 PHE D 159 TRP 0.014 0.002 TRP F 101 HIS 0.005 0.001 HIS F 278 Details of bonding type rmsd covalent geometry : bond 0.00416 (17218) covalent geometry : angle 0.67755 (23655) hydrogen bonds : bond 0.04589 ( 751) hydrogen bonds : angle 5.15025 ( 2112) metal coordination : bond 0.00958 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.610 Fit side-chains REVERT: E 95 MET cc_start: 0.7627 (ttm) cc_final: 0.7281 (ttm) REVERT: E 249 LEU cc_start: 0.8669 (tt) cc_final: 0.8048 (mt) REVERT: E 262 MET cc_start: 0.8465 (mmm) cc_final: 0.7887 (mpm) REVERT: E 715 MET cc_start: 0.5493 (OUTLIER) cc_final: 0.4727 (mtp) REVERT: E 729 TYR cc_start: 0.4244 (t80) cc_final: 0.3222 (t80) REVERT: E 734 LEU cc_start: 0.6431 (mm) cc_final: 0.6165 (mt) REVERT: A 69 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6664 (ttpp) REVERT: A 102 ASN cc_start: 0.7811 (t0) cc_final: 0.7561 (t0) REVERT: A 232 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6840 (mp0) REVERT: A 236 LEU cc_start: 0.7862 (tp) cc_final: 0.7659 (tt) REVERT: A 241 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7615 (mp) REVERT: B 226 ARG cc_start: 0.7354 (ptt90) cc_final: 0.7119 (ptm-80) REVERT: B 242 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: C 69 LYS cc_start: 0.7930 (tppt) cc_final: 0.7657 (mppt) REVERT: C 118 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7069 (mp) REVERT: C 147 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7642 (mtt90) REVERT: D 123 MET cc_start: 0.7271 (tmm) cc_final: 0.6988 (tmm) REVERT: D 260 GLN cc_start: 0.6206 (OUTLIER) cc_final: 0.5767 (pm20) REVERT: F 104 LEU cc_start: 0.8661 (mm) cc_final: 0.8176 (mm) REVERT: F 115 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: F 130 LYS cc_start: 0.8226 (tttt) cc_final: 0.7592 (tttm) REVERT: F 142 VAL cc_start: 0.7807 (t) cc_final: 0.7595 (p) REVERT: F 144 LYS cc_start: 0.8351 (mmmm) cc_final: 0.7815 (mmtm) REVERT: F 148 ILE cc_start: 0.8611 (mp) cc_final: 0.8304 (pp) REVERT: F 191 MET cc_start: 0.7168 (mtm) cc_final: 0.6906 (mtp) REVERT: F 209 MET cc_start: 0.7675 (mmt) cc_final: 0.7268 (mmt) REVERT: F 214 TYR cc_start: 0.7175 (m-80) cc_final: 0.6728 (m-10) REVERT: F 330 ASN cc_start: 0.6785 (m-40) cc_final: 0.6393 (m-40) outliers start: 42 outliers final: 24 residues processed: 217 average time/residue: 0.4922 time to fit residues: 120.6067 Evaluate side-chains 209 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 510 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 309 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 161 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 184 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 177 optimal weight: 0.0670 chunk 194 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 727 GLN B 107 GLN D 56 ASN F 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090757 restraints weight = 29535.041| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.23 r_work: 0.3137 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17220 Z= 0.141 Angle : 0.651 11.987 23655 Z= 0.322 Chirality : 0.043 0.162 2768 Planarity : 0.005 0.050 2821 Dihedral : 14.896 178.254 3190 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.77 % Allowed : 25.88 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.19), residues: 1991 helix: 1.15 (0.18), residues: 862 sheet: -0.83 (0.25), residues: 353 loop : -0.45 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 226 TYR 0.039 0.002 TYR F 137 PHE 0.019 0.002 PHE D 159 TRP 0.012 0.002 TRP E 659 HIS 0.003 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00324 (17218) covalent geometry : angle 0.65054 (23655) hydrogen bonds : bond 0.04214 ( 751) hydrogen bonds : angle 5.08031 ( 2112) metal coordination : bond 0.00165 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5564.90 seconds wall clock time: 95 minutes 48.57 seconds (5748.57 seconds total)