Starting phenix.real_space_refine on Tue Dec 31 21:31:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ey1_50051/12_2024/9ey1_50051.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ey1_50051/12_2024/9ey1_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_50051/12_2024/9ey1_50051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ey1_50051/12_2024/9ey1_50051.map" model { file = "/net/cci-nas-00/data/ceres_data/9ey1_50051/12_2024/9ey1_50051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ey1_50051/12_2024/9ey1_50051.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 11.74, per 1000 atoms: 0.70 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: 4.56 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 6.06 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: 6.85 Time building geometry restraints manager: 5.13 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: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 50.220 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.990 ------------------------------------------------------------------------------- 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 : 0.004 0.168 17218 Z= 0.289 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.019 0.001 TRP E 433 HIS 0.009 0.001 HIS E 546 PHE 0.014 0.001 PHE F 384 TYR 0.028 0.001 TYR F 132 ARG 0.009 0.000 ARG E 785 *********************** 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 : 1.683 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: 0.7499 (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: 0.6990 (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: 0.6905 (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: 0.6952 (mttt) REVERT: C 242 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6459 (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: 1.3061 time to fit residues: 578.4373 Evaluate side-chains 260 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 172 optimal weight: 3.9990 chunk 154 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 143 GLN F 200 GLN F 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17218 Z= 0.232 Angle : 0.661 8.085 23655 Z= 0.333 Chirality : 0.044 0.164 2768 Planarity : 0.005 0.052 2821 Dihedral : 15.586 177.349 3218 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.61 % Allowed : 20.22 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.011 0.002 TRP F 183 HIS 0.005 0.001 HIS F 278 PHE 0.016 0.002 PHE E 521 TYR 0.015 0.002 TYR E 729 ARG 0.006 0.001 ARG E 46 *********************** 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 323 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 248 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 138 LEU cc_start: 0.8120 (mp) cc_final: 0.7848 (mm) REVERT: E 145 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7687 (mp0) REVERT: E 174 GLU cc_start: 0.7815 (tp30) cc_final: 0.7608 (tp30) REVERT: E 249 LEU cc_start: 0.8732 (tt) cc_final: 0.8096 (mt) REVERT: E 262 MET cc_start: 0.8413 (mmm) cc_final: 0.8047 (mpm) REVERT: E 309 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7946 (m) REVERT: E 449 GLU cc_start: 0.8911 (tp30) cc_final: 0.8607 (tp30) REVERT: E 479 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6629 (tm130) REVERT: E 524 LEU cc_start: 0.8312 (mt) cc_final: 0.8020 (mt) REVERT: E 588 LEU cc_start: 0.7767 (mm) cc_final: 0.7539 (mt) REVERT: E 715 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5272 (mtp) REVERT: E 720 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7874 (mp) REVERT: E 760 MET cc_start: 0.8106 (mmm) cc_final: 0.7723 (mmm) REVERT: E 777 GLU cc_start: 0.8605 (tt0) cc_final: 0.8162 (tm-30) REVERT: E 778 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6885 (mtp) REVERT: A 28 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6168 (tt0) REVERT: A 40 LEU cc_start: 0.7281 (tt) cc_final: 0.6778 (tm) REVERT: A 52 LYS cc_start: 0.6990 (tptp) cc_final: 0.6756 (tmmt) REVERT: A 84 ARG cc_start: 0.7542 (ptm160) cc_final: 0.7211 (ptm160) REVERT: A 102 ASN cc_start: 0.7107 (t0) cc_final: 0.6793 (t0) REVERT: A 112 GLU cc_start: 0.6674 (mp0) cc_final: 0.6361 (mm-30) REVERT: A 118 LEU cc_start: 0.6539 (mp) cc_final: 0.6239 (mm) REVERT: A 123 MET cc_start: 0.7183 (ttp) cc_final: 0.6629 (tmm) REVERT: A 211 GLU cc_start: 0.5833 (pm20) cc_final: 0.5611 (pm20) REVERT: A 232 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6218 (mp0) REVERT: A 242 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6426 (mt-10) REVERT: B 69 LYS cc_start: 0.6587 (tptp) cc_final: 0.6261 (tttt) REVERT: B 99 LYS cc_start: 0.7114 (mtmt) cc_final: 0.6831 (mtpp) REVERT: B 143 GLN cc_start: 0.6499 (pm20) cc_final: 0.5996 (mp10) REVERT: B 242 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6326 (mp0) REVERT: C 48 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7104 (tp30) REVERT: C 52 LYS cc_start: 0.7528 (tppt) cc_final: 0.7174 (ttmp) REVERT: C 69 LYS cc_start: 0.7545 (tppt) cc_final: 0.6945 (mtmm) REVERT: C 104 LYS cc_start: 0.7388 (tttt) cc_final: 0.7091 (ttmt) REVERT: C 118 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6305 (mp) REVERT: C 147 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7743 (mtt90) REVERT: C 212 LYS cc_start: 0.7488 (mtmm) cc_final: 0.7189 (mttt) REVERT: C 251 ILE cc_start: 0.7977 (mt) cc_final: 0.7707 (mm) REVERT: D 48 GLU cc_start: 0.6548 (pm20) cc_final: 0.6151 (mp0) REVERT: D 56 ASN cc_start: 0.7463 (p0) cc_final: 0.7180 (p0) REVERT: D 69 LYS cc_start: 0.7391 (ttpp) cc_final: 0.7189 (tttm) REVERT: D 79 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5810 (tppt) REVERT: D 81 LYS cc_start: 0.7119 (tmtm) cc_final: 0.6806 (tmtt) REVERT: D 84 ARG cc_start: 0.6801 (ptm-80) cc_final: 0.6186 (ptp90) REVERT: D 86 ASP cc_start: 0.6822 (m-30) cc_final: 0.6600 (m-30) REVERT: D 96 VAL cc_start: 0.6428 (OUTLIER) cc_final: 0.6190 (p) REVERT: D 110 THR cc_start: 0.7554 (OUTLIER) cc_final: 0.7170 (p) REVERT: D 123 MET cc_start: 0.6652 (tmm) cc_final: 0.6287 (tmm) REVERT: D 159 PHE cc_start: 0.5853 (m-80) cc_final: 0.5305 (m-80) REVERT: D 236 LEU cc_start: 0.7419 (tp) cc_final: 0.7201 (tp) REVERT: D 260 GLN cc_start: 0.4707 (OUTLIER) cc_final: 0.4199 (pm20) REVERT: F 104 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8344 (tm) REVERT: F 120 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8313 (mt) REVERT: F 129 LYS cc_start: 0.8748 (mttp) cc_final: 0.8457 (mmmt) REVERT: F 130 LYS cc_start: 0.8218 (tttt) cc_final: 0.7631 (tttm) REVERT: F 132 TYR cc_start: 0.7725 (t80) cc_final: 0.7484 (t80) REVERT: F 159 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8270 (mm-30) REVERT: F 191 MET cc_start: 0.7409 (mtm) cc_final: 0.7080 (mtp) REVERT: F 209 MET cc_start: 0.7653 (mmt) cc_final: 0.7098 (mmt) REVERT: F 214 TYR cc_start: 0.7123 (m-80) cc_final: 0.6691 (m-10) REVERT: F 217 ARG cc_start: 0.7040 (tpt-90) cc_final: 0.6684 (tmt-80) REVERT: F 221 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6359 (tp40) REVERT: F 250 ILE cc_start: 0.7126 (mt) cc_final: 0.6816 (tp) REVERT: F 276 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7771 (mppt) REVERT: F 327 LYS cc_start: 0.7877 (mttm) cc_final: 0.7609 (mmpt) REVERT: F 360 LEU cc_start: 0.7821 (mt) cc_final: 0.7569 (mt) outliers start: 75 outliers final: 19 residues processed: 301 average time/residue: 1.2337 time to fit residues: 418.0431 Evaluate side-chains 236 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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 309 VAL 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 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 79 LYS Chi-restraints excluded: chain D residue 96 VAL 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 102 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 51 optimal weight: 0.0270 chunk 185 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 C 44 ASN C 162 GLN C 220 GLN D 102 ASN F 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17218 Z= 0.211 Angle : 0.613 9.666 23655 Z= 0.306 Chirality : 0.043 0.178 2768 Planarity : 0.005 0.050 2821 Dihedral : 15.277 178.099 3193 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.67 % Allowed : 20.65 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1991 helix: 1.10 (0.18), residues: 857 sheet: -0.37 (0.26), residues: 341 loop : -0.22 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 183 HIS 0.004 0.001 HIS D 109 PHE 0.017 0.002 PHE F 179 TYR 0.017 0.002 TYR F 137 ARG 0.003 0.000 ARG A 84 *********************** 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 297 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 221 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 MET cc_start: 0.7587 (ttm) cc_final: 0.7292 (ttm) REVERT: E 99 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8136 (tppt) REVERT: E 138 LEU cc_start: 0.8104 (mp) cc_final: 0.7827 (mm) REVERT: E 145 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7910 (mp0) REVERT: E 249 LEU cc_start: 0.8769 (tt) cc_final: 0.8131 (mt) REVERT: E 262 MET cc_start: 0.8415 (mmm) cc_final: 0.8069 (mpm) REVERT: E 449 GLU cc_start: 0.8938 (tp30) cc_final: 0.8645 (tp30) REVERT: E 479 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6532 (tm130) REVERT: E 524 LEU cc_start: 0.8271 (mt) cc_final: 0.8034 (mt) REVERT: E 588 LEU cc_start: 0.7678 (mm) cc_final: 0.7463 (mt) REVERT: E 668 MET cc_start: 0.7047 (pmm) cc_final: 0.6811 (pmm) REVERT: E 720 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7890 (mp) REVERT: E 771 PHE cc_start: 0.7889 (m-80) cc_final: 0.7601 (m-80) REVERT: E 777 GLU cc_start: 0.8609 (tt0) cc_final: 0.8130 (tm-30) REVERT: E 783 GLU cc_start: 0.9200 (tt0) cc_final: 0.8885 (tp30) REVERT: A 28 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6151 (tt0) REVERT: A 40 LEU cc_start: 0.7219 (tt) cc_final: 0.6764 (tm) REVERT: A 52 LYS cc_start: 0.6989 (tptp) cc_final: 0.6679 (mptt) REVERT: A 69 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.6183 (ttpp) REVERT: A 70 ASP cc_start: 0.6526 (m-30) cc_final: 0.5926 (m-30) REVERT: A 84 ARG cc_start: 0.7570 (ptm160) cc_final: 0.7194 (ptm160) REVERT: A 102 ASN cc_start: 0.7070 (t0) cc_final: 0.6812 (t0) REVERT: A 112 GLU cc_start: 0.6689 (mp0) cc_final: 0.6358 (mm-30) REVERT: A 118 LEU cc_start: 0.6528 (mp) cc_final: 0.6229 (mm) REVERT: A 123 MET cc_start: 0.7124 (ttp) cc_final: 0.6534 (tmm) REVERT: A 211 GLU cc_start: 0.5906 (pm20) cc_final: 0.5645 (pm20) REVERT: A 232 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6317 (mp0) REVERT: A 236 LEU cc_start: 0.7289 (tp) cc_final: 0.6881 (tp) REVERT: A 242 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6470 (mt-10) REVERT: B 48 GLU cc_start: 0.7164 (tp30) cc_final: 0.6808 (tp30) REVERT: B 79 LYS cc_start: 0.6677 (tptt) cc_final: 0.6189 (ttmm) REVERT: B 99 LYS cc_start: 0.7065 (mtmt) cc_final: 0.6713 (mtpp) REVERT: B 111 LEU cc_start: 0.6731 (tp) cc_final: 0.6444 (tp) REVERT: B 142 ASP cc_start: 0.5624 (p0) cc_final: 0.5216 (p0) REVERT: B 143 GLN cc_start: 0.6461 (pm20) cc_final: 0.6006 (mp10) REVERT: B 226 ARG cc_start: 0.7438 (ptt90) cc_final: 0.7228 (ptm-80) REVERT: B 242 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6445 (mp0) REVERT: C 48 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7046 (tp30) REVERT: C 52 LYS cc_start: 0.7452 (tppt) cc_final: 0.7089 (ttmp) REVERT: C 69 LYS cc_start: 0.7532 (tppt) cc_final: 0.6931 (mtmm) REVERT: C 96 VAL cc_start: 0.7510 (OUTLIER) cc_final: 0.7231 (p) REVERT: C 104 LYS cc_start: 0.7322 (tttt) cc_final: 0.7040 (ttmt) REVERT: C 118 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6339 (mp) REVERT: C 119 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6572 (m-30) REVERT: C 147 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7682 (mtt90) REVERT: C 189 ILE cc_start: 0.6918 (mt) cc_final: 0.6666 (mt) REVERT: C 212 LYS cc_start: 0.7585 (mtmm) cc_final: 0.7209 (mptt) REVERT: C 251 ILE cc_start: 0.7984 (mt) cc_final: 0.7703 (mm) REVERT: D 48 GLU cc_start: 0.6548 (pm20) cc_final: 0.6239 (mp0) REVERT: D 79 LYS cc_start: 0.6377 (OUTLIER) cc_final: 0.5954 (tppt) REVERT: D 81 LYS cc_start: 0.7094 (tmtm) cc_final: 0.6640 (mmmm) REVERT: D 84 ARG cc_start: 0.6727 (ptm-80) cc_final: 0.6152 (ptp90) REVERT: D 110 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7193 (p) REVERT: D 123 MET cc_start: 0.6660 (tmm) cc_final: 0.6257 (tmm) REVERT: D 143 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: D 260 GLN cc_start: 0.4768 (OUTLIER) cc_final: 0.4322 (pm20) REVERT: F 104 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8325 (tm) REVERT: F 130 LYS cc_start: 0.8202 (tttt) cc_final: 0.7591 (tttm) REVERT: F 191 MET cc_start: 0.7346 (mtm) cc_final: 0.7050 (mtp) REVERT: F 209 MET cc_start: 0.7571 (mmt) cc_final: 0.7051 (mmt) REVERT: F 214 TYR cc_start: 0.7177 (m-80) cc_final: 0.6711 (m-10) REVERT: F 217 ARG cc_start: 0.6843 (tpt-90) cc_final: 0.6494 (tpt90) REVERT: F 250 ILE cc_start: 0.7088 (mt) cc_final: 0.6799 (tp) REVERT: F 276 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7813 (mppt) REVERT: F 327 LYS cc_start: 0.7843 (mttm) cc_final: 0.7603 (mmpt) REVERT: F 330 ASN cc_start: 0.7045 (m-40) cc_final: 0.6621 (m-40) outliers start: 76 outliers final: 30 residues processed: 278 average time/residue: 1.3363 time to fit residues: 413.9972 Evaluate side-chains 242 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain E residue 256 VAL 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 720 ILE Chi-restraints excluded: chain E residue 732 VAL 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 C residue 53 LYS Chi-restraints excluded: chain C residue 96 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 79 LYS 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 207 THR Chi-restraints excluded: chain D residue 260 GLN 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 Chi-restraints excluded: chain F residue 376 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.0570 chunk 139 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 0.0270 chunk 124 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 176 optimal weight: 0.1980 chunk 53 optimal weight: 0.1980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 505 ASN B 107 GLN C 44 ASN D 56 ASN F 162 ASN F 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17218 Z= 0.150 Angle : 0.558 8.053 23655 Z= 0.277 Chirality : 0.041 0.194 2768 Planarity : 0.005 0.049 2821 Dihedral : 14.978 177.163 3192 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.38 % Allowed : 21.82 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1991 helix: 1.41 (0.18), residues: 850 sheet: -0.35 (0.27), residues: 331 loop : -0.22 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 659 HIS 0.004 0.001 HIS E 552 PHE 0.021 0.001 PHE E 306 TYR 0.021 0.001 TYR F 137 ARG 0.006 0.000 ARG E 526 *********************** 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 284 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 1.857 Fit side-chains revert: symmetry clash REVERT: E 79 GLU cc_start: 0.8084 (tp30) cc_final: 0.7665 (mm-30) REVERT: E 86 ASN cc_start: 0.6907 (m-40) cc_final: 0.6699 (m-40) REVERT: E 95 MET cc_start: 0.7563 (ttm) cc_final: 0.7207 (ttm) REVERT: E 99 LYS cc_start: 0.8443 (mmtp) cc_final: 0.8041 (tppt) REVERT: E 138 LEU cc_start: 0.8118 (mp) cc_final: 0.7850 (mm) REVERT: E 145 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7961 (mp0) REVERT: E 249 LEU cc_start: 0.8687 (tt) cc_final: 0.8034 (mt) REVERT: E 449 GLU cc_start: 0.8915 (tp30) cc_final: 0.8622 (tp30) REVERT: E 479 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6526 (tm130) REVERT: E 504 VAL cc_start: 0.7631 (t) cc_final: 0.7354 (t) REVERT: E 524 LEU cc_start: 0.8234 (mt) cc_final: 0.8033 (mt) REVERT: E 588 LEU cc_start: 0.7695 (mm) cc_final: 0.7438 (mt) REVERT: E 610 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6940 (mm) REVERT: E 668 MET cc_start: 0.7184 (pmm) cc_final: 0.6806 (pmm) REVERT: E 771 PHE cc_start: 0.7806 (m-80) cc_final: 0.7506 (m-80) REVERT: E 777 GLU cc_start: 0.8602 (tt0) cc_final: 0.8120 (tm-30) REVERT: E 783 GLU cc_start: 0.9218 (tt0) cc_final: 0.8926 (tp30) REVERT: A 28 GLU cc_start: 0.6410 (mt-10) cc_final: 0.6075 (tt0) REVERT: A 40 LEU cc_start: 0.7241 (tt) cc_final: 0.7022 (tt) REVERT: A 52 LYS cc_start: 0.6951 (tptp) cc_final: 0.6660 (mptt) REVERT: A 70 ASP cc_start: 0.6507 (m-30) cc_final: 0.5939 (m-30) REVERT: A 84 ARG cc_start: 0.7498 (ptm160) cc_final: 0.7284 (ptm160) REVERT: A 102 ASN cc_start: 0.7092 (t0) cc_final: 0.6726 (t0) REVERT: A 112 GLU cc_start: 0.6724 (mp0) cc_final: 0.6398 (mm-30) REVERT: A 118 LEU cc_start: 0.6559 (mp) cc_final: 0.6253 (mm) REVERT: A 123 MET cc_start: 0.7129 (ttp) cc_final: 0.6539 (tmm) REVERT: A 211 GLU cc_start: 0.5890 (pm20) cc_final: 0.5614 (pm20) REVERT: A 232 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6384 (mp0) REVERT: A 236 LEU cc_start: 0.7291 (tp) cc_final: 0.7091 (tt) REVERT: A 242 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6454 (mt-10) REVERT: B 48 GLU cc_start: 0.7137 (tp30) cc_final: 0.6787 (tp30) REVERT: B 52 LYS cc_start: 0.7181 (mtpp) cc_final: 0.6853 (mtpp) REVERT: B 69 LYS cc_start: 0.7131 (tttt) cc_final: 0.6850 (ttpp) REVERT: B 79 LYS cc_start: 0.6668 (tptt) cc_final: 0.6092 (ttmm) REVERT: B 99 LYS cc_start: 0.7086 (mtmt) cc_final: 0.6737 (mtpp) REVERT: B 104 LYS cc_start: 0.7303 (mtmm) cc_final: 0.6557 (mmmm) REVERT: B 111 LEU cc_start: 0.6647 (tp) cc_final: 0.6302 (tp) REVERT: B 116 ARG cc_start: 0.6855 (ttp-110) cc_final: 0.6502 (ttp-110) REVERT: B 140 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7254 (mm-30) REVERT: B 142 ASP cc_start: 0.5540 (p0) cc_final: 0.5173 (p0) REVERT: B 143 GLN cc_start: 0.6484 (pm20) cc_final: 0.6021 (mp10) REVERT: B 226 ARG cc_start: 0.7430 (ptt90) cc_final: 0.7183 (ptm-80) REVERT: B 242 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6412 (mp0) REVERT: C 52 LYS cc_start: 0.7540 (tppt) cc_final: 0.7174 (ttmp) REVERT: C 69 LYS cc_start: 0.7475 (tppt) cc_final: 0.6944 (mtmm) REVERT: C 104 LYS cc_start: 0.7361 (tttt) cc_final: 0.7049 (tttt) REVERT: C 123 MET cc_start: 0.6712 (tmm) cc_final: 0.6466 (tmm) REVERT: C 147 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7697 (mtt90) REVERT: C 189 ILE cc_start: 0.6907 (mt) cc_final: 0.6593 (mt) REVERT: C 212 LYS cc_start: 0.7565 (mtmm) cc_final: 0.7306 (mttt) REVERT: C 251 ILE cc_start: 0.7994 (mt) cc_final: 0.7710 (mm) REVERT: D 48 GLU cc_start: 0.6346 (pm20) cc_final: 0.6056 (mp0) REVERT: D 79 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5988 (tppt) REVERT: D 81 LYS cc_start: 0.6997 (tmtm) cc_final: 0.6564 (mmmm) REVERT: D 84 ARG cc_start: 0.6716 (ptm-80) cc_final: 0.6256 (ptp90) REVERT: D 123 MET cc_start: 0.6656 (tmm) cc_final: 0.6335 (tmm) REVERT: D 236 LEU cc_start: 0.7450 (tp) cc_final: 0.7213 (tp) REVERT: F 130 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7560 (mttt) REVERT: F 148 ILE cc_start: 0.8444 (mp) cc_final: 0.8189 (pp) REVERT: F 191 MET cc_start: 0.7301 (mtm) cc_final: 0.7041 (mtp) REVERT: F 209 MET cc_start: 0.7555 (mmt) cc_final: 0.7008 (mmt) REVERT: F 214 TYR cc_start: 0.7196 (m-80) cc_final: 0.6764 (m-10) REVERT: F 217 ARG cc_start: 0.6844 (tpt-90) cc_final: 0.6548 (tpt90) REVERT: F 276 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7828 (mppt) REVERT: F 327 LYS cc_start: 0.7882 (mttm) cc_final: 0.7628 (mmpt) REVERT: F 330 ASN cc_start: 0.6874 (m-40) cc_final: 0.6431 (m-40) outliers start: 55 outliers final: 21 residues processed: 269 average time/residue: 1.3035 time to fit residues: 391.2441 Evaluate side-chains 230 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 172 GLU 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 503 LEU 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 732 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 189 ILE 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 14 VAL 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 79 LYS Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN C 44 ASN D 56 ASN F 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17218 Z= 0.287 Angle : 0.649 8.451 23655 Z= 0.326 Chirality : 0.044 0.145 2768 Planarity : 0.005 0.056 2821 Dihedral : 15.057 179.505 3191 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.61 % Allowed : 21.45 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1991 helix: 1.06 (0.18), residues: 857 sheet: -0.68 (0.26), residues: 338 loop : -0.35 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 587 HIS 0.006 0.001 HIS F 278 PHE 0.017 0.002 PHE D 159 TYR 0.022 0.002 TYR E 729 ARG 0.008 0.001 ARG A 84 *********************** 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 289 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 214 time to evaluate : 1.838 Fit side-chains REVERT: E 79 GLU cc_start: 0.8128 (tp30) cc_final: 0.7841 (mm-30) REVERT: E 95 MET cc_start: 0.7516 (ttm) cc_final: 0.7110 (ttm) REVERT: E 99 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8289 (tppt) REVERT: E 138 LEU cc_start: 0.8084 (mp) cc_final: 0.7814 (mm) REVERT: E 249 LEU cc_start: 0.8807 (tt) cc_final: 0.8197 (mt) REVERT: E 262 MET cc_start: 0.8102 (mmm) cc_final: 0.7726 (mpm) REVERT: E 449 GLU cc_start: 0.8963 (tp30) cc_final: 0.8643 (tp30) REVERT: E 479 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6523 (tm130) REVERT: E 524 LEU cc_start: 0.8211 (mt) cc_final: 0.7959 (mt) REVERT: E 588 LEU cc_start: 0.7694 (mm) cc_final: 0.7469 (mt) REVERT: E 610 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.7022 (mm) REVERT: E 668 MET cc_start: 0.7173 (pmm) cc_final: 0.6870 (pmm) REVERT: E 771 PHE cc_start: 0.7798 (m-80) cc_final: 0.7488 (m-80) REVERT: E 777 GLU cc_start: 0.8595 (tt0) cc_final: 0.8182 (tm-30) REVERT: E 783 GLU cc_start: 0.9187 (tt0) cc_final: 0.8928 (tp30) REVERT: A 28 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6144 (tt0) REVERT: A 40 LEU cc_start: 0.6848 (tt) cc_final: 0.6419 (tm) REVERT: A 52 LYS cc_start: 0.6994 (tptp) cc_final: 0.6518 (mptt) REVERT: A 69 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.6224 (ttpp) REVERT: A 70 ASP cc_start: 0.6576 (m-30) cc_final: 0.6034 (m-30) REVERT: A 102 ASN cc_start: 0.6900 (t0) cc_final: 0.6516 (t0) REVERT: A 112 GLU cc_start: 0.6555 (mp0) cc_final: 0.6168 (mp0) REVERT: A 118 LEU cc_start: 0.6447 (mp) cc_final: 0.6162 (mm) REVERT: A 123 MET cc_start: 0.7135 (ttp) cc_final: 0.6483 (tmm) REVERT: A 232 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6459 (mp0) REVERT: A 241 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7384 (mp) REVERT: B 48 GLU cc_start: 0.7098 (tp30) cc_final: 0.6781 (tp30) REVERT: B 79 LYS cc_start: 0.6657 (tptt) cc_final: 0.6119 (ttmm) REVERT: B 99 LYS cc_start: 0.7026 (mtmt) cc_final: 0.6602 (mtpp) REVERT: B 104 LYS cc_start: 0.7171 (mtmm) cc_final: 0.6633 (mmmm) REVERT: B 142 ASP cc_start: 0.5536 (p0) cc_final: 0.5154 (p0) REVERT: B 143 GLN cc_start: 0.6457 (pm20) cc_final: 0.6021 (mp10) REVERT: B 242 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6271 (mp0) REVERT: C 52 LYS cc_start: 0.7453 (tppt) cc_final: 0.7038 (ttmp) REVERT: C 69 LYS cc_start: 0.7674 (tppt) cc_final: 0.7067 (mppt) REVERT: C 96 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7211 (p) REVERT: C 104 LYS cc_start: 0.7459 (tttt) cc_final: 0.7107 (tttt) REVERT: C 118 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6333 (mp) REVERT: C 212 LYS cc_start: 0.7480 (mtmm) cc_final: 0.7150 (mptt) REVERT: C 251 ILE cc_start: 0.7968 (mt) cc_final: 0.7708 (mm) REVERT: D 79 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.5963 (tppt) REVERT: D 81 LYS cc_start: 0.7044 (tmtm) cc_final: 0.6711 (tmtt) REVERT: D 123 MET cc_start: 0.6548 (tmm) cc_final: 0.6229 (tmm) REVERT: D 143 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: D 260 GLN cc_start: 0.4878 (OUTLIER) cc_final: 0.4443 (pm20) REVERT: F 104 LEU cc_start: 0.8670 (mm) cc_final: 0.8238 (tm) REVERT: F 115 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: F 117 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8179 (mt) REVERT: F 129 LYS cc_start: 0.8618 (mttp) cc_final: 0.8406 (mmtt) REVERT: F 130 LYS cc_start: 0.8209 (tttt) cc_final: 0.7613 (mttt) REVERT: F 148 ILE cc_start: 0.8415 (mp) cc_final: 0.8129 (pp) REVERT: F 191 MET cc_start: 0.7350 (mtm) cc_final: 0.7082 (mtp) REVERT: F 209 MET cc_start: 0.7598 (mmt) cc_final: 0.7095 (mmt) REVERT: F 214 TYR cc_start: 0.7170 (m-80) cc_final: 0.6733 (m-10) REVERT: F 217 ARG cc_start: 0.6917 (tpt-90) cc_final: 0.6604 (tmt-80) REVERT: F 327 LYS cc_start: 0.7876 (mttm) cc_final: 0.7604 (mmpt) REVERT: F 330 ASN cc_start: 0.7049 (m-40) cc_final: 0.6621 (m-40) outliers start: 75 outliers final: 36 residues processed: 271 average time/residue: 1.2762 time to fit residues: 387.5692 Evaluate side-chains 243 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 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 512 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 732 VAL Chi-restraints excluded: chain E residue 759 THR 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 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 205 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 211 GLU 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 79 LYS Chi-restraints excluded: chain D residue 104 LYS 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 115 GLU Chi-restraints excluded: chain F residue 117 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 66 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 115 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 197 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN C 44 ASN D 56 ASN F 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17218 Z= 0.197 Angle : 0.596 8.485 23655 Z= 0.297 Chirality : 0.042 0.153 2768 Planarity : 0.005 0.051 2821 Dihedral : 14.949 178.503 3191 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.50 % Allowed : 23.11 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1991 helix: 1.19 (0.18), residues: 862 sheet: -0.74 (0.26), residues: 338 loop : -0.36 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 587 HIS 0.004 0.001 HIS D 109 PHE 0.020 0.002 PHE D 159 TYR 0.025 0.002 TYR E 729 ARG 0.006 0.000 ARG B 226 *********************** 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 270 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 2.459 Fit side-chains revert: symmetry clash REVERT: E 86 ASN cc_start: 0.7051 (m-40) cc_final: 0.6809 (m-40) REVERT: E 95 MET cc_start: 0.7542 (ttm) cc_final: 0.7115 (ttm) REVERT: E 99 LYS cc_start: 0.8568 (mmtp) cc_final: 0.8271 (tppt) REVERT: E 138 LEU cc_start: 0.8085 (mp) cc_final: 0.7810 (mm) REVERT: E 249 LEU cc_start: 0.8853 (tt) cc_final: 0.8205 (mt) REVERT: E 262 MET cc_start: 0.8234 (mmm) cc_final: 0.7808 (mpm) REVERT: E 416 MET cc_start: 0.7602 (pp-130) cc_final: 0.7360 (pp-130) REVERT: E 449 GLU cc_start: 0.8970 (tp30) cc_final: 0.8651 (tp30) REVERT: E 479 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: E 524 LEU cc_start: 0.8150 (mt) cc_final: 0.7914 (mt) REVERT: E 588 LEU cc_start: 0.7683 (mm) cc_final: 0.7449 (mt) REVERT: E 610 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7012 (mm) REVERT: E 668 MET cc_start: 0.7226 (pmm) cc_final: 0.6980 (pmm) REVERT: E 727 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6728 (pp30) REVERT: E 734 LEU cc_start: 0.6392 (tm) cc_final: 0.5519 (mt) REVERT: E 735 PHE cc_start: 0.6145 (m-80) cc_final: 0.5800 (m-80) REVERT: E 771 PHE cc_start: 0.7764 (m-80) cc_final: 0.7432 (m-80) REVERT: E 777 GLU cc_start: 0.8594 (tt0) cc_final: 0.8238 (tm-30) REVERT: E 783 GLU cc_start: 0.9174 (tt0) cc_final: 0.8960 (tp30) REVERT: A 20 SER cc_start: 0.6752 (p) cc_final: 0.6469 (m) REVERT: A 28 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6163 (tt0) REVERT: A 52 LYS cc_start: 0.7082 (tptp) cc_final: 0.6632 (mptt) REVERT: A 69 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.6166 (ttpp) REVERT: A 70 ASP cc_start: 0.6618 (m-30) cc_final: 0.6032 (m-30) REVERT: A 84 ARG cc_start: 0.7444 (ptm160) cc_final: 0.7049 (ptm160) REVERT: A 102 ASN cc_start: 0.6955 (t0) cc_final: 0.6609 (t0) REVERT: A 112 GLU cc_start: 0.6561 (mp0) cc_final: 0.6265 (mm-30) REVERT: A 118 LEU cc_start: 0.6490 (mp) cc_final: 0.6188 (mm) REVERT: A 123 MET cc_start: 0.7056 (ttp) cc_final: 0.6483 (tmm) REVERT: A 232 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6484 (mp0) REVERT: B 48 GLU cc_start: 0.7089 (tp30) cc_final: 0.6752 (tp30) REVERT: B 79 LYS cc_start: 0.6652 (tptt) cc_final: 0.6106 (ttmm) REVERT: B 99 LYS cc_start: 0.7043 (mtmt) cc_final: 0.6632 (mtpp) REVERT: B 104 LYS cc_start: 0.7184 (mtmm) cc_final: 0.6625 (mmmm) REVERT: B 142 ASP cc_start: 0.5496 (p0) cc_final: 0.5122 (p0) REVERT: B 143 GLN cc_start: 0.6458 (pm20) cc_final: 0.6025 (mp10) REVERT: B 205 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5347 (tt) REVERT: B 226 ARG cc_start: 0.7499 (ptt90) cc_final: 0.7209 (ptm-80) REVERT: B 242 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6228 (mp0) REVERT: C 52 LYS cc_start: 0.7487 (tppt) cc_final: 0.7090 (ttmp) REVERT: C 69 LYS cc_start: 0.7682 (tppt) cc_final: 0.7089 (mppt) REVERT: C 96 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7198 (p) REVERT: C 104 LYS cc_start: 0.7453 (tttt) cc_final: 0.7089 (tttt) REVERT: C 118 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6314 (mp) REVERT: C 147 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7662 (mtt90) REVERT: C 212 LYS cc_start: 0.7572 (mtmm) cc_final: 0.7249 (mptt) REVERT: C 251 ILE cc_start: 0.7984 (mt) cc_final: 0.7705 (mm) REVERT: D 48 GLU cc_start: 0.6392 (pm20) cc_final: 0.5965 (mp0) REVERT: D 79 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.5888 (tppt) REVERT: D 81 LYS cc_start: 0.7089 (tmtm) cc_final: 0.6751 (tmtt) REVERT: D 123 MET cc_start: 0.6671 (tmm) cc_final: 0.6360 (tmm) REVERT: F 104 LEU cc_start: 0.8740 (mm) cc_final: 0.8356 (tm) REVERT: F 115 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: F 130 LYS cc_start: 0.8254 (tttt) cc_final: 0.7638 (mttt) REVERT: F 144 LYS cc_start: 0.8177 (mmmm) cc_final: 0.7642 (mmtm) REVERT: F 148 ILE cc_start: 0.8474 (mp) cc_final: 0.8189 (pp) REVERT: F 191 MET cc_start: 0.7244 (mtm) cc_final: 0.6995 (mtp) REVERT: F 209 MET cc_start: 0.7558 (mmt) cc_final: 0.7068 (mmt) REVERT: F 214 TYR cc_start: 0.7174 (m-80) cc_final: 0.6725 (m-10) REVERT: F 217 ARG cc_start: 0.6869 (tpt-90) cc_final: 0.6602 (tmt-80) REVERT: F 327 LYS cc_start: 0.7776 (mttm) cc_final: 0.7524 (mmpt) REVERT: F 330 ASN cc_start: 0.7016 (m-40) cc_final: 0.6565 (m-40) outliers start: 57 outliers final: 29 residues processed: 259 average time/residue: 1.2749 time to fit residues: 370.3582 Evaluate side-chains 239 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 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 512 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 727 GLN Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain A residue 16 THR 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 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 132 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN B 107 GLN D 56 ASN F 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17218 Z= 0.227 Angle : 0.615 8.440 23655 Z= 0.307 Chirality : 0.043 0.156 2768 Planarity : 0.005 0.054 2821 Dihedral : 14.941 178.814 3191 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.30 % Allowed : 22.56 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1991 helix: 1.15 (0.18), residues: 865 sheet: -0.76 (0.26), residues: 338 loop : -0.40 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 587 HIS 0.004 0.001 HIS D 109 PHE 0.019 0.002 PHE D 159 TYR 0.028 0.002 TYR E 729 ARG 0.005 0.001 ARG B 226 *********************** 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 277 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 207 time to evaluate : 1.865 Fit side-chains REVERT: E 86 ASN cc_start: 0.7059 (m-40) cc_final: 0.6819 (m-40) REVERT: E 95 MET cc_start: 0.7551 (ttm) cc_final: 0.7096 (ttm) REVERT: E 99 LYS cc_start: 0.8569 (mmtp) cc_final: 0.8319 (tppt) REVERT: E 138 LEU cc_start: 0.8047 (mp) cc_final: 0.7768 (mm) REVERT: E 249 LEU cc_start: 0.8854 (tt) cc_final: 0.8213 (mt) REVERT: E 449 GLU cc_start: 0.8961 (tp30) cc_final: 0.8639 (tp30) REVERT: E 479 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6532 (tm130) REVERT: E 524 LEU cc_start: 0.8138 (mt) cc_final: 0.7907 (mt) REVERT: E 588 LEU cc_start: 0.7692 (mm) cc_final: 0.7459 (mt) REVERT: E 610 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6991 (mm) REVERT: E 668 MET cc_start: 0.7390 (pmm) cc_final: 0.7114 (pmm) REVERT: E 734 LEU cc_start: 0.6358 (tm) cc_final: 0.5524 (mm) REVERT: E 735 PHE cc_start: 0.6128 (m-80) cc_final: 0.5705 (m-80) REVERT: E 771 PHE cc_start: 0.7839 (m-80) cc_final: 0.7491 (m-80) REVERT: E 777 GLU cc_start: 0.8625 (tt0) cc_final: 0.8277 (tm-30) REVERT: A 20 SER cc_start: 0.6588 (p) cc_final: 0.6328 (m) REVERT: A 28 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6281 (tt0) REVERT: A 40 LEU cc_start: 0.6664 (tt) cc_final: 0.6353 (tm) REVERT: A 52 LYS cc_start: 0.6991 (tptp) cc_final: 0.6529 (mptt) REVERT: A 69 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.6189 (ttpp) REVERT: A 70 ASP cc_start: 0.6576 (m-30) cc_final: 0.6063 (m-30) REVERT: A 102 ASN cc_start: 0.6883 (t0) cc_final: 0.6551 (t0) REVERT: A 112 GLU cc_start: 0.6549 (mp0) cc_final: 0.6257 (mm-30) REVERT: A 118 LEU cc_start: 0.6465 (mp) cc_final: 0.6163 (mm) REVERT: A 123 MET cc_start: 0.7137 (ttp) cc_final: 0.6489 (tmm) REVERT: B 48 GLU cc_start: 0.6987 (tp30) cc_final: 0.6711 (tp30) REVERT: B 79 LYS cc_start: 0.6646 (tptt) cc_final: 0.6100 (ttmm) REVERT: B 99 LYS cc_start: 0.7025 (mtmt) cc_final: 0.6608 (mtpp) REVERT: B 104 LYS cc_start: 0.7155 (mtmm) cc_final: 0.6609 (mmmm) REVERT: B 142 ASP cc_start: 0.5478 (p0) cc_final: 0.5155 (p0) REVERT: B 143 GLN cc_start: 0.6447 (pm20) cc_final: 0.6048 (mp10) REVERT: B 159 PHE cc_start: 0.5836 (m-80) cc_final: 0.4652 (t80) REVERT: B 205 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5236 (tt) REVERT: B 226 ARG cc_start: 0.7399 (ptt90) cc_final: 0.7114 (ptm-80) REVERT: B 242 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6263 (mp0) REVERT: B 249 GLU cc_start: 0.5747 (OUTLIER) cc_final: 0.5424 (tm-30) REVERT: C 52 LYS cc_start: 0.7458 (tppt) cc_final: 0.7063 (ttmp) REVERT: C 69 LYS cc_start: 0.7697 (tppt) cc_final: 0.7089 (mppt) REVERT: C 96 VAL cc_start: 0.7473 (OUTLIER) cc_final: 0.7174 (p) REVERT: C 104 LYS cc_start: 0.7469 (tttt) cc_final: 0.7109 (tttt) REVERT: C 118 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6434 (mp) REVERT: C 147 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7643 (mtt90) REVERT: C 212 LYS cc_start: 0.7575 (mtmm) cc_final: 0.7256 (mptt) REVERT: C 251 ILE cc_start: 0.7974 (mt) cc_final: 0.7711 (mm) REVERT: D 48 GLU cc_start: 0.6431 (pm20) cc_final: 0.6039 (mp0) REVERT: D 79 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6021 (tppt) REVERT: D 81 LYS cc_start: 0.7091 (tmtm) cc_final: 0.6761 (tmtt) REVERT: D 123 MET cc_start: 0.6548 (tmm) cc_final: 0.6235 (tmm) REVERT: D 260 GLN cc_start: 0.4740 (OUTLIER) cc_final: 0.4281 (pm20) REVERT: F 104 LEU cc_start: 0.8789 (mm) cc_final: 0.8410 (tm) REVERT: F 115 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: F 130 LYS cc_start: 0.8334 (tttt) cc_final: 0.7614 (mttm) REVERT: F 144 LYS cc_start: 0.8195 (mmmm) cc_final: 0.7717 (mmtm) REVERT: F 148 ILE cc_start: 0.8472 (mp) cc_final: 0.8182 (pp) REVERT: F 191 MET cc_start: 0.7216 (mtm) cc_final: 0.6957 (mtp) REVERT: F 209 MET cc_start: 0.7548 (mmt) cc_final: 0.7033 (mmt) REVERT: F 214 TYR cc_start: 0.7222 (m-80) cc_final: 0.6769 (m-10) REVERT: F 217 ARG cc_start: 0.6847 (tpt-90) cc_final: 0.6575 (tmt-80) REVERT: F 327 LYS cc_start: 0.7807 (mttm) cc_final: 0.7457 (mmpt) REVERT: F 330 ASN cc_start: 0.7052 (m-40) cc_final: 0.6614 (m-40) outliers start: 70 outliers final: 35 residues processed: 260 average time/residue: 1.2806 time to fit residues: 373.1882 Evaluate side-chains 238 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 1.909 ------------------------------------------------------------------------------- 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 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 512 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 732 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 56 ASN 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 16 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 69 LYS 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 B residue 214 CYS Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 104 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 17218 Z= 0.402 Angle : 0.756 10.428 23655 Z= 0.381 Chirality : 0.048 0.165 2768 Planarity : 0.006 0.055 2821 Dihedral : 15.186 178.023 3191 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.67 % Allowed : 22.68 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 1991 helix: 0.66 (0.17), residues: 883 sheet: -0.94 (0.26), residues: 337 loop : -0.70 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 587 HIS 0.008 0.002 HIS F 278 PHE 0.021 0.003 PHE A 223 TYR 0.035 0.003 TYR E 729 ARG 0.009 0.001 ARG A 84 *********************** 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 280 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 204 time to evaluate : 1.745 Fit side-chains REVERT: E 79 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: E 95 MET cc_start: 0.7558 (ttm) cc_final: 0.7118 (ttm) REVERT: E 99 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8390 (tppt) REVERT: E 138 LEU cc_start: 0.7983 (mp) cc_final: 0.7667 (mm) REVERT: E 249 LEU cc_start: 0.8846 (tt) cc_final: 0.8270 (mt) REVERT: E 262 MET cc_start: 0.8140 (mmm) cc_final: 0.7563 (mpm) REVERT: E 284 ILE cc_start: 0.8065 (tp) cc_final: 0.7832 (pt) REVERT: E 449 GLU cc_start: 0.8968 (tp30) cc_final: 0.8651 (tp30) REVERT: E 479 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6523 (tm130) REVERT: E 524 LEU cc_start: 0.8135 (mt) cc_final: 0.7897 (mt) REVERT: E 610 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7038 (mm) REVERT: E 715 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5275 (mtp) REVERT: E 734 LEU cc_start: 0.6431 (tm) cc_final: 0.5464 (mt) REVERT: E 735 PHE cc_start: 0.6329 (m-80) cc_final: 0.5822 (m-80) REVERT: E 771 PHE cc_start: 0.7817 (m-80) cc_final: 0.7484 (m-80) REVERT: E 777 GLU cc_start: 0.8691 (tt0) cc_final: 0.8372 (tm-30) REVERT: A 20 SER cc_start: 0.6628 (p) cc_final: 0.6376 (m) REVERT: A 28 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6431 (tt0) REVERT: A 52 LYS cc_start: 0.6935 (tptp) cc_final: 0.6542 (mptt) REVERT: A 69 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6247 (ttpp) REVERT: A 102 ASN cc_start: 0.6845 (t0) cc_final: 0.6497 (t0) REVERT: A 112 GLU cc_start: 0.6610 (mp0) cc_final: 0.6200 (mp0) REVERT: A 118 LEU cc_start: 0.6297 (mp) cc_final: 0.5985 (mm) REVERT: A 123 MET cc_start: 0.7137 (ttp) cc_final: 0.6485 (tmm) REVERT: A 185 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6616 (t0) REVERT: A 232 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5818 (mp0) REVERT: B 48 GLU cc_start: 0.7123 (tp30) cc_final: 0.6817 (tp30) REVERT: B 79 LYS cc_start: 0.6738 (tptt) cc_final: 0.6191 (ttmm) REVERT: B 99 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6477 (mtpp) REVERT: B 104 LYS cc_start: 0.7021 (mtmm) cc_final: 0.6633 (mmmm) REVERT: B 142 ASP cc_start: 0.5625 (p0) cc_final: 0.5350 (p0) REVERT: B 143 GLN cc_start: 0.6403 (pm20) cc_final: 0.6074 (mp10) REVERT: B 242 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6351 (mp0) REVERT: B 249 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5472 (tm-30) REVERT: C 48 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6817 (tp30) REVERT: C 52 LYS cc_start: 0.7398 (tppt) cc_final: 0.7182 (tppt) REVERT: C 69 LYS cc_start: 0.7759 (tppt) cc_final: 0.7089 (mppt) REVERT: C 96 VAL cc_start: 0.7523 (OUTLIER) cc_final: 0.7185 (p) REVERT: C 104 LYS cc_start: 0.7430 (tttt) cc_final: 0.7097 (ttmt) REVERT: C 118 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6471 (mp) REVERT: C 147 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7616 (mtt90) REVERT: C 212 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7089 (mptt) REVERT: C 251 ILE cc_start: 0.7879 (mt) cc_final: 0.7646 (mm) REVERT: D 79 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6027 (tppt) REVERT: D 81 LYS cc_start: 0.7031 (tmtm) cc_final: 0.6778 (tmtt) REVERT: D 123 MET cc_start: 0.6493 (tmm) cc_final: 0.5820 (tmm) REVERT: D 260 GLN cc_start: 0.4796 (OUTLIER) cc_final: 0.4374 (pm20) REVERT: F 104 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8359 (tm) REVERT: F 107 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7093 (mt-10) REVERT: F 115 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: F 129 LYS cc_start: 0.8639 (mttp) cc_final: 0.8334 (mmtt) REVERT: F 130 LYS cc_start: 0.8344 (tttt) cc_final: 0.7650 (tttm) REVERT: F 144 LYS cc_start: 0.8224 (mmmm) cc_final: 0.7669 (mmtm) REVERT: F 148 ILE cc_start: 0.8490 (mp) cc_final: 0.8172 (pp) REVERT: F 191 MET cc_start: 0.7292 (mtm) cc_final: 0.7044 (mtp) REVERT: F 214 TYR cc_start: 0.7244 (m-80) cc_final: 0.6741 (m-10) REVERT: F 217 ARG cc_start: 0.6895 (tpt-90) cc_final: 0.6618 (tpt90) REVERT: F 327 LYS cc_start: 0.7775 (mttm) cc_final: 0.7513 (mmtm) outliers start: 76 outliers final: 42 residues processed: 264 average time/residue: 1.3168 time to fit residues: 390.0902 Evaluate side-chains 253 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 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 555 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 636 GLU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 727 GLN 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 31 VAL Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 211 GLU 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 79 LYS Chi-restraints excluded: chain D residue 104 LYS 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 115 GLU Chi-restraints excluded: chain F residue 120 LEU 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 309 ILE 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 188 optimal weight: 0.3980 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 0.2980 chunk 110 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 390 ASN E 727 GLN B 107 GLN D 56 ASN F 221 GLN F 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17218 Z= 0.221 Angle : 0.647 10.716 23655 Z= 0.323 Chirality : 0.043 0.399 2768 Planarity : 0.005 0.050 2821 Dihedral : 15.008 179.697 3191 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.56 % Allowed : 23.91 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1991 helix: 1.05 (0.18), residues: 859 sheet: -0.94 (0.25), residues: 353 loop : -0.51 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 587 HIS 0.004 0.001 HIS D 109 PHE 0.021 0.002 PHE D 159 TYR 0.028 0.002 TYR F 137 ARG 0.006 0.000 ARG B 226 *********************** 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 264 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 1.844 Fit side-chains REVERT: E 86 ASN cc_start: 0.7030 (m-40) cc_final: 0.6795 (m-40) REVERT: E 95 MET cc_start: 0.7536 (ttm) cc_final: 0.7110 (ttm) REVERT: E 99 LYS cc_start: 0.8591 (mmtp) cc_final: 0.8366 (tppt) REVERT: E 138 LEU cc_start: 0.8020 (mp) cc_final: 0.7712 (mm) REVERT: E 249 LEU cc_start: 0.8852 (tt) cc_final: 0.8267 (mt) REVERT: E 262 MET cc_start: 0.8154 (mmm) cc_final: 0.7525 (mpm) REVERT: E 284 ILE cc_start: 0.8047 (tp) cc_final: 0.7806 (pt) REVERT: E 449 GLU cc_start: 0.8962 (tp30) cc_final: 0.8641 (tp30) REVERT: E 479 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6473 (tm130) REVERT: E 524 LEU cc_start: 0.8114 (mt) cc_final: 0.7886 (mt) REVERT: E 610 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6968 (mm) REVERT: E 715 MET cc_start: 0.5544 (OUTLIER) cc_final: 0.4865 (mtp) REVERT: E 727 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7055 (pp30) REVERT: E 734 LEU cc_start: 0.6249 (tm) cc_final: 0.5872 (mt) REVERT: E 735 PHE cc_start: 0.6153 (m-80) cc_final: 0.5794 (m-80) REVERT: E 771 PHE cc_start: 0.7952 (m-80) cc_final: 0.7602 (m-80) REVERT: E 777 GLU cc_start: 0.8684 (tt0) cc_final: 0.8407 (tm-30) REVERT: A 20 SER cc_start: 0.6617 (p) cc_final: 0.6360 (m) REVERT: A 28 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6316 (tt0) REVERT: A 40 LEU cc_start: 0.6800 (tt) cc_final: 0.6451 (tm) REVERT: A 52 LYS cc_start: 0.6989 (tptp) cc_final: 0.6530 (mptt) REVERT: A 64 ASP cc_start: 0.6317 (t0) cc_final: 0.5989 (t70) REVERT: A 69 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.6184 (ttpp) REVERT: A 70 ASP cc_start: 0.6503 (m-30) cc_final: 0.5927 (m-30) REVERT: A 102 ASN cc_start: 0.6859 (t0) cc_final: 0.6547 (t0) REVERT: A 112 GLU cc_start: 0.6495 (mp0) cc_final: 0.6153 (mp0) REVERT: A 118 LEU cc_start: 0.6476 (mp) cc_final: 0.6179 (mm) REVERT: A 123 MET cc_start: 0.7123 (ttp) cc_final: 0.6507 (tmm) REVERT: A 232 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5816 (mp0) REVERT: A 236 LEU cc_start: 0.7254 (tp) cc_final: 0.6819 (tp) REVERT: B 48 GLU cc_start: 0.7086 (tp30) cc_final: 0.6792 (tp30) REVERT: B 79 LYS cc_start: 0.6682 (tptt) cc_final: 0.6120 (ttmm) REVERT: B 99 LYS cc_start: 0.7018 (mtmt) cc_final: 0.6580 (mtpp) REVERT: B 104 LYS cc_start: 0.7015 (mtmm) cc_final: 0.6610 (mmmm) REVERT: B 143 GLN cc_start: 0.6425 (pm20) cc_final: 0.6077 (mp10) REVERT: B 226 ARG cc_start: 0.7445 (ptt90) cc_final: 0.7150 (ptm-80) REVERT: B 242 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6335 (mp0) REVERT: B 251 ILE cc_start: 0.7303 (mp) cc_final: 0.6814 (mm) REVERT: C 52 LYS cc_start: 0.7522 (tppt) cc_final: 0.7094 (ttmp) REVERT: C 69 LYS cc_start: 0.7723 (tppt) cc_final: 0.7112 (mppt) REVERT: C 96 VAL cc_start: 0.7519 (OUTLIER) cc_final: 0.7197 (p) REVERT: C 104 LYS cc_start: 0.7419 (tttt) cc_final: 0.7088 (ttmt) REVERT: C 118 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6517 (mp) REVERT: C 147 ARG cc_start: 0.7955 (mtt90) cc_final: 0.7560 (mtt90) REVERT: C 212 LYS cc_start: 0.7507 (mtmm) cc_final: 0.7130 (mptt) REVERT: C 251 ILE cc_start: 0.7976 (mt) cc_final: 0.7699 (mm) REVERT: D 48 GLU cc_start: 0.6433 (pm20) cc_final: 0.6026 (mp0) REVERT: D 79 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.6033 (tppt) REVERT: D 123 MET cc_start: 0.6548 (tmm) cc_final: 0.5837 (tmm) REVERT: D 260 GLN cc_start: 0.4713 (OUTLIER) cc_final: 0.4285 (pm20) REVERT: F 101 TRP cc_start: 0.7666 (OUTLIER) cc_final: 0.7170 (m100) REVERT: F 104 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8326 (mm) REVERT: F 115 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: F 130 LYS cc_start: 0.8317 (tttt) cc_final: 0.7687 (mttm) REVERT: F 144 LYS cc_start: 0.8229 (mmmm) cc_final: 0.7775 (mmtm) REVERT: F 147 GLN cc_start: 0.7584 (mm-40) cc_final: 0.6821 (mt0) REVERT: F 148 ILE cc_start: 0.8482 (mp) cc_final: 0.8177 (pp) REVERT: F 191 MET cc_start: 0.7220 (mtm) cc_final: 0.6959 (mtp) REVERT: F 214 TYR cc_start: 0.7216 (m-80) cc_final: 0.6713 (m-10) REVERT: F 217 ARG cc_start: 0.6886 (tpt-90) cc_final: 0.6601 (tpt90) REVERT: F 327 LYS cc_start: 0.7823 (mttm) cc_final: 0.7553 (mmtm) REVERT: F 330 ASN cc_start: 0.6964 (m-40) cc_final: 0.6566 (m-40) outliers start: 58 outliers final: 30 residues processed: 253 average time/residue: 1.2698 time to fit residues: 360.2260 Evaluate side-chains 243 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 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 510 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 560 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 636 GLU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 727 GLN Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 69 LYS 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 C residue 16 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 120 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 91 optimal weight: 0.0070 chunk 134 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN D 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17218 Z= 0.201 Angle : 0.629 10.568 23655 Z= 0.312 Chirality : 0.043 0.325 2768 Planarity : 0.005 0.053 2821 Dihedral : 14.923 178.677 3191 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.83 % Allowed : 24.83 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 1991 helix: 1.17 (0.18), residues: 860 sheet: -0.87 (0.26), residues: 343 loop : -0.42 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 587 HIS 0.005 0.001 HIS E 552 PHE 0.021 0.002 PHE D 159 TYR 0.028 0.002 TYR E 729 ARG 0.006 0.000 ARG B 226 ********************** 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 250 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 1.888 Fit side-chains REVERT: E 95 MET cc_start: 0.7533 (ttm) cc_final: 0.7083 (ttm) REVERT: E 99 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8321 (tppt) REVERT: E 138 LEU cc_start: 0.7969 (mp) cc_final: 0.7649 (mm) REVERT: E 249 LEU cc_start: 0.8850 (tt) cc_final: 0.8269 (mt) REVERT: E 262 MET cc_start: 0.8270 (mmm) cc_final: 0.7845 (mpm) REVERT: E 284 ILE cc_start: 0.8162 (tp) cc_final: 0.7857 (pt) REVERT: E 449 GLU cc_start: 0.8955 (tp30) cc_final: 0.8624 (tp30) REVERT: E 479 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6501 (tm130) REVERT: E 524 LEU cc_start: 0.8087 (mt) cc_final: 0.7861 (mt) REVERT: E 610 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6998 (mm) REVERT: E 715 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.4825 (mtp) REVERT: E 727 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6785 (pp30) REVERT: E 729 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5566 (t80) REVERT: E 734 LEU cc_start: 0.6622 (tm) cc_final: 0.5933 (mt) REVERT: E 735 PHE cc_start: 0.6343 (m-80) cc_final: 0.5921 (m-80) REVERT: E 771 PHE cc_start: 0.7762 (m-80) cc_final: 0.7368 (m-80) REVERT: E 777 GLU cc_start: 0.8690 (tt0) cc_final: 0.8417 (tm-30) REVERT: A 20 SER cc_start: 0.6603 (p) cc_final: 0.6361 (m) REVERT: A 28 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6309 (tt0) REVERT: A 52 LYS cc_start: 0.7085 (tptp) cc_final: 0.6644 (mptt) REVERT: A 64 ASP cc_start: 0.6329 (t0) cc_final: 0.6000 (t70) REVERT: A 69 LYS cc_start: 0.6371 (OUTLIER) cc_final: 0.6161 (ttpp) REVERT: A 70 ASP cc_start: 0.6478 (m-30) cc_final: 0.5985 (m-30) REVERT: A 102 ASN cc_start: 0.6844 (t0) cc_final: 0.6499 (t0) REVERT: A 112 GLU cc_start: 0.6573 (mp0) cc_final: 0.6232 (mp0) REVERT: A 118 LEU cc_start: 0.6493 (mp) cc_final: 0.6180 (mm) REVERT: A 123 MET cc_start: 0.7145 (ttp) cc_final: 0.6492 (tmm) REVERT: A 211 GLU cc_start: 0.6296 (pm20) cc_final: 0.6056 (pm20) REVERT: A 232 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5819 (mp0) REVERT: B 48 GLU cc_start: 0.7081 (tp30) cc_final: 0.6783 (tp30) REVERT: B 79 LYS cc_start: 0.6675 (tptt) cc_final: 0.6117 (ttmm) REVERT: B 99 LYS cc_start: 0.7034 (mtmt) cc_final: 0.6600 (mtpp) REVERT: B 104 LYS cc_start: 0.7100 (mtmm) cc_final: 0.6647 (mmmm) REVERT: B 226 ARG cc_start: 0.7445 (ptt90) cc_final: 0.7151 (ptm-80) REVERT: B 242 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6334 (mp0) REVERT: B 251 ILE cc_start: 0.7224 (mp) cc_final: 0.6803 (mm) REVERT: C 52 LYS cc_start: 0.7523 (tppt) cc_final: 0.7126 (ttmp) REVERT: C 69 LYS cc_start: 0.7719 (tppt) cc_final: 0.7110 (mppt) REVERT: C 96 VAL cc_start: 0.7584 (OUTLIER) cc_final: 0.7270 (p) REVERT: C 104 LYS cc_start: 0.7419 (tttt) cc_final: 0.7084 (ttmt) REVERT: C 118 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6535 (mp) REVERT: C 147 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7530 (mtt90) REVERT: C 212 LYS cc_start: 0.7534 (mtmm) cc_final: 0.7173 (mptt) REVERT: C 251 ILE cc_start: 0.7976 (mt) cc_final: 0.7693 (mm) REVERT: D 48 GLU cc_start: 0.6456 (pm20) cc_final: 0.6033 (mp0) REVERT: D 79 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6020 (tppt) REVERT: D 123 MET cc_start: 0.6549 (tmm) cc_final: 0.5852 (tmm) REVERT: D 260 GLN cc_start: 0.4716 (OUTLIER) cc_final: 0.4263 (pm20) REVERT: F 101 TRP cc_start: 0.7544 (OUTLIER) cc_final: 0.7116 (m100) REVERT: F 104 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8249 (mm) REVERT: F 115 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: F 130 LYS cc_start: 0.8307 (tttt) cc_final: 0.7666 (mttm) REVERT: F 137 TYR cc_start: 0.8061 (t80) cc_final: 0.7410 (t80) REVERT: F 144 LYS cc_start: 0.8186 (mmmm) cc_final: 0.7771 (mmtm) REVERT: F 147 GLN cc_start: 0.7611 (mm-40) cc_final: 0.6835 (mt0) REVERT: F 148 ILE cc_start: 0.8480 (mp) cc_final: 0.8178 (pp) REVERT: F 191 MET cc_start: 0.7229 (mtm) cc_final: 0.6957 (mtp) REVERT: F 214 TYR cc_start: 0.7205 (m-80) cc_final: 0.6722 (m-10) REVERT: F 217 ARG cc_start: 0.6818 (tpt-90) cc_final: 0.6568 (tpt90) REVERT: F 327 LYS cc_start: 0.7752 (mttm) cc_final: 0.7506 (mmtm) REVERT: F 330 ASN cc_start: 0.6939 (m-40) cc_final: 0.6496 (m-40) outliers start: 46 outliers final: 27 residues processed: 241 average time/residue: 1.3232 time to fit residues: 360.7117 Evaluate side-chains 245 residues out of total 1629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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 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 510 THR Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 560 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 636 GLU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 727 GLN Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain E residue 759 THR Chi-restraints excluded: chain A residue 16 THR 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 232 GLU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.0020 chunk 142 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 GLN B 107 GLN D 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090248 restraints weight = 29701.282| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.26 r_work: 0.3129 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17218 Z= 0.252 Angle : 0.667 13.358 23655 Z= 0.332 Chirality : 0.044 0.306 2768 Planarity : 0.005 0.050 2821 Dihedral : 14.948 179.184 3191 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.07 % Allowed : 24.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1991 helix: 1.12 (0.18), residues: 860 sheet: -0.91 (0.26), residues: 343 loop : -0.47 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 587 HIS 0.005 0.001 HIS E 552 PHE 0.023 0.002 PHE F 97 TYR 0.024 0.002 TYR E 729 ARG 0.007 0.001 ARG E 788 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6452.27 seconds wall clock time: 116 minutes 57.53 seconds (7017.53 seconds total)