Starting phenix.real_space_refine on Sat Sep 12 11:25:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi5_23840/09_2026/7mi5_23840_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi5_23840/09_2026/7mi5_23840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mi5_23840/09_2026/7mi5_23840_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi5_23840/09_2026/7mi5_23840_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mi5_23840/09_2026/7mi5_23840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi5_23840/09_2026/7mi5_23840.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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: 7 Type Number sf(0) Gaussians Mn 6 7.51 5 Fe 4 7.16 5 P 60 5.49 5 S 87 5.16 5 C 9573 2.51 5 N 2847 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15469 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4347 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 35, 'TRANS': 517} Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2711 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "C" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2887 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 22, 'TRANS': 339} Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "H" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 134 SG CYS A 22 58.998 39.159 120.263 1.00121.43 S ATOM 1460 SG CYS A 196 60.316 44.706 121.026 1.00115.75 S ATOM 1421 SG CYS A 190 56.911 44.316 116.691 1.00122.55 S ATOM 1397 SG CYS A 187 61.613 42.265 116.734 1.00110.23 S Restraints were copied for chains: D, F Time building chain proxies: 3.99, per 1000 atoms: 0.26 Number of scatterers: 15469 At special positions: 0 Unit cell: (94.71, 105.78, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Mn 6 24.99 S 87 16.00 P 60 15.00 O 2892 8.00 N 2847 7.00 C 9573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 617.2 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 601 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 22 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 187 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 196 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 190 " Number of angles added : 12 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3282 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 18 sheets defined 51.0% alpha, 12.9% beta 16 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.509A pdb=" N TYR A 21 " --> pdb=" O ASN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.693A pdb=" N ARG A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 4.226A pdb=" N ALA A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 Processing helix chain 'A' and resid 155 through 175 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.599A pdb=" N ARG A 189 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 353 through 369 removed outlier: 3.611A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 392 removed outlier: 4.241A pdb=" N SER A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 7.180A pdb=" N ARG A 396 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.566A pdb=" N ARG A 410 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 441 removed outlier: 3.867A pdb=" N GLU A 433 " --> pdb=" O MET A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.968A pdb=" N GLU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 483 removed outlier: 4.664A pdb=" N LEU A 471 " --> pdb=" O PRO A 467 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 301 through 316 removed outlier: 3.654A pdb=" N GLU B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 343 removed outlier: 3.536A pdb=" N CYS B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 370 removed outlier: 3.788A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 392 removed outlier: 3.815A pdb=" N HIS B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 417 through 441 Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.689A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 501 through 518 Processing helix chain 'B' and resid 531 through 546 removed outlier: 3.628A pdb=" N GLU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 549 No H-bonds generated for 'chain 'B' and resid 547 through 549' Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 316 through 343 Processing helix chain 'C' and resid 353 through 369 removed outlier: 3.610A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 392 removed outlier: 4.240A pdb=" N SER C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 398 removed outlier: 7.180A pdb=" N ARG C 396 " --> pdb=" O ARG C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.567A pdb=" N ARG C 410 " --> pdb=" O PHE C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 441 removed outlier: 3.867A pdb=" N GLU C 433 " --> pdb=" O MET C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 removed outlier: 3.967A pdb=" N GLU C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 483 removed outlier: 4.664A pdb=" N LEU C 471 " --> pdb=" O PRO C 467 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 489 No H-bonds generated for 'chain 'C' and resid 487 through 489' Processing helix chain 'C' and resid 501 through 517 Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 301 through 316 removed outlier: 3.653A pdb=" N GLU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 343 removed outlier: 3.535A pdb=" N CYS D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 370 removed outlier: 3.787A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 370 " --> pdb=" O HIS D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 392 removed outlier: 3.814A pdb=" N HIS D 390 " --> pdb=" O ARG D 386 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 417 through 441 Processing helix chain 'D' and resid 458 through 466 removed outlier: 3.688A pdb=" N GLU D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 Processing helix chain 'D' and resid 487 through 489 No H-bonds generated for 'chain 'D' and resid 487 through 489' Processing helix chain 'D' and resid 501 through 518 Processing helix chain 'D' and resid 531 through 546 removed outlier: 3.629A pdb=" N GLU D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 549 No H-bonds generated for 'chain 'D' and resid 547 through 549' Processing helix chain 'E' and resid 13 through 26 Processing helix chain 'E' and resid 41 through 52 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'F' and resid 13 through 26 Processing helix chain 'F' and resid 41 through 52 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.047A pdb=" N ILE A 11 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LYS A 85 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 73 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.912A pdb=" N VAL A 96 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ALA A 139 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR A 141 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP A 100 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.771A pdb=" N LEU A 222 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA A 261 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 224 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE A 263 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 226 " --> pdb=" O PHE A 263 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N THR A 284 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 260 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 286 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 262 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL A 283 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 297 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS B 295 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 294 " --> pdb=" O TRP B 285 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR B 284 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 260 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU B 286 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 262 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 222 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN B 259 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 253 removed outlier: 5.401A pdb=" N ARG A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU A 244 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 493 Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 521 Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 251 removed outlier: 3.604A pdb=" N ALA B 250 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AA9, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AB1, first strand: chain 'C' and resid 222 through 226 removed outlier: 6.771A pdb=" N LEU C 222 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ALA C 261 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU C 224 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE C 263 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL C 226 " --> pdb=" O PHE C 263 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N THR C 284 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 260 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU C 286 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU C 262 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL C 283 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL C 297 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS D 295 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 294 " --> pdb=" O TRP D 285 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR D 284 " --> pdb=" O SER D 258 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 260 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU D 286 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU D 262 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 222 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN D 259 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 247 through 253 removed outlier: 5.401A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU C 244 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 491 through 493 Processing sheet with id=AB4, first strand: chain 'C' and resid 519 through 521 Processing sheet with id=AB5, first strand: chain 'D' and resid 248 through 251 removed outlier: 3.603A pdb=" N ALA D 250 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 491 through 493 Processing sheet with id=AB7, first strand: chain 'D' and resid 519 through 520 Processing sheet with id=AB8, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.486A pdb=" N VAL E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY E 69 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE E 6 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASP E 67 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N SER E 8 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE E 65 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP E 10 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL E 63 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 78 through 80 removed outlier: 5.162A pdb=" N VAL F 63 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP F 10 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE F 65 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER F 8 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASP F 67 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE F 6 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY F 69 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) 733 hydrogen bonds defined for protein. 2115 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 6894 1.42 - 1.63: 8898 1.63 - 1.85: 137 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 15941 Sorted by residual: bond pdb=" C1' DG H 20 " pdb=" N9 DG H 20 " ideal model delta sigma weight residual 1.468 1.360 0.108 1.40e-02 5.10e+03 5.94e+01 bond pdb=" C1' DA H 21 " pdb=" N9 DA H 21 " ideal model delta sigma weight residual 1.468 1.368 0.100 1.40e-02 5.10e+03 5.06e+01 bond pdb=" C1' DC H 19 " pdb=" N1 DC H 19 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" N1 DC G 15 " pdb=" C6 DC G 15 " ideal model delta sigma weight residual 1.367 1.343 0.024 6.00e-03 2.78e+04 1.64e+01 bond pdb=" C3' DC H 15 " pdb=" C2' DC H 15 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.56e+01 ... (remaining 15936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.40: 21697 6.40 - 12.80: 112 12.80 - 19.20: 17 19.20 - 25.60: 5 25.60 - 32.00: 4 Bond angle restraints: 21835 Sorted by residual: angle pdb=" CA MET D 364 " pdb=" CB MET D 364 " pdb=" CG MET D 364 " ideal model delta sigma weight residual 114.10 139.65 -25.55 2.00e+00 2.50e-01 1.63e+02 angle pdb=" CA MET B 364 " pdb=" CB MET B 364 " pdb=" CG MET B 364 " ideal model delta sigma weight residual 114.10 139.62 -25.52 2.00e+00 2.50e-01 1.63e+02 angle pdb=" CA MET D 479 " pdb=" CB MET D 479 " pdb=" CG MET D 479 " ideal model delta sigma weight residual 114.10 137.14 -23.04 2.00e+00 2.50e-01 1.33e+02 angle pdb=" CA MET B 479 " pdb=" CB MET B 479 " pdb=" CG MET B 479 " ideal model delta sigma weight residual 114.10 137.14 -23.04 2.00e+00 2.50e-01 1.33e+02 angle pdb=" CB MET B 479 " pdb=" CG MET B 479 " pdb=" SD MET B 479 " ideal model delta sigma weight residual 112.70 144.70 -32.00 3.00e+00 1.11e-01 1.14e+02 ... (remaining 21830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.22: 8506 29.22 - 58.43: 797 58.43 - 87.65: 103 87.65 - 116.87: 4 116.87 - 146.08: 2 Dihedral angle restraints: 9412 sinusoidal: 4289 harmonic: 5123 Sorted by residual: dihedral pdb=" CA ARG B 412 " pdb=" C ARG B 412 " pdb=" N ARG B 413 " pdb=" CA ARG B 413 " ideal model delta harmonic sigma weight residual -180.00 -145.33 -34.67 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA ARG D 412 " pdb=" C ARG D 412 " pdb=" N ARG D 413 " pdb=" CA ARG D 413 " ideal model delta harmonic sigma weight residual -180.00 -145.36 -34.64 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CA GLN C 312 " pdb=" C GLN C 312 " pdb=" N ARG C 313 " pdb=" CA ARG C 313 " ideal model delta harmonic sigma weight residual 180.00 149.32 30.68 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 9409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1974 0.084 - 0.169: 331 0.169 - 0.253: 47 0.253 - 0.338: 7 0.338 - 0.422: 2 Chirality restraints: 2361 Sorted by residual: chirality pdb=" CA MET B 364 " pdb=" N MET B 364 " pdb=" C MET B 364 " pdb=" CB MET B 364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA MET D 364 " pdb=" N MET D 364 " pdb=" C MET D 364 " pdb=" CB MET D 364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA TYR A 232 " pdb=" N TYR A 232 " pdb=" C TYR A 232 " pdb=" CB TYR A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2358 not shown) Planarity restraints: 2644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 327 " 0.029 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP D 327 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP D 327 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP D 327 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 327 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 327 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 327 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 327 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 327 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 327 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 327 " -0.029 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP B 327 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP B 327 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP B 327 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 327 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 327 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 327 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 327 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 327 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 327 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 340 " 0.061 9.50e-02 1.11e+02 3.44e-02 5.96e+00 pdb=" NE ARG B 340 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 340 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG B 340 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 340 " -0.012 2.00e-02 2.50e+03 ... (remaining 2641 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 124 2.31 - 2.96: 8814 2.96 - 3.60: 25515 3.60 - 4.25: 38226 4.25 - 4.90: 60951 Nonbonded interactions: 133630 Sorted by model distance: nonbonded pdb=" N2 DG G 8 " pdb=" N3 DG H 20 " model vdw 1.662 3.200 nonbonded pdb=" OP1 DG H 32 " pdb="MN MN H 801 " model vdw 1.716 2.320 nonbonded pdb=" N GLY A 237 " pdb=" OP1 DT G 6 " model vdw 1.916 3.120 nonbonded pdb=" NE2 HIS A 48 " pdb="MN MN H 801 " model vdw 1.916 2.400 nonbonded pdb=" C2 DG G 8 " pdb=" C2 DG H 20 " model vdw 1.925 3.480 ... (remaining 133625 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 'B' and resid 219 through 558) selection = (chain 'C' and resid 219 through 558) selection = (chain 'D' and resid 219 through 558) } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 0.750 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: 0.150 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.280 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 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 : 0.010 0.362 15945 Z= 0.554 Angle : 1.615 60.520 21847 Z= 0.825 Chirality : 0.065 0.422 2361 Planarity : 0.006 0.045 2644 Dihedral : 21.219 146.085 6130 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 35.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.42 % Favored : 90.47 % Rotamer: Outliers : 11.95 % Allowed : 2.28 % Favored : 85.77 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.18), residues: 1773 helix: -1.06 (0.16), residues: 822 sheet: -0.81 (0.46), residues: 124 loop : -2.33 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.003 ARG B 340 TYR 0.026 0.003 TYR C 311 PHE 0.021 0.003 PHE D 491 TRP 0.078 0.004 TRP D 327 HIS 0.017 0.002 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00977 / 0.55 (15941) covalent geometry : angle 1.47905 / 0.82 (21835) hydrogen bonds : bond 0.17744 / 12.16 ( 770) hydrogen bonds : angle 8.00788 / 5.71 ( 2169) metal coordination : bond 0.18912 / 11.76 ( 4) metal coordination : angle 27.70161 / 14.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 483 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.7512 (t70) cc_final: 0.7238 (t70) REVERT: A 143 VAL cc_start: 0.8024 (t) cc_final: 0.6934 (t) REVERT: A 154 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.5555 (t70) REVERT: A 256 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7268 (tt0) REVERT: A 358 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5847 (ppp) REVERT: A 420 ASN cc_start: 0.6853 (OUTLIER) cc_final: 0.6280 (m-40) REVERT: A 557 VAL cc_start: 0.8015 (t) cc_final: 0.7710 (t) REVERT: B 220 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5359 (mmm160) REVERT: B 227 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6216 (mm-40) REVERT: B 248 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5936 (ttp80) REVERT: B 351 LYS cc_start: 0.6667 (tptp) cc_final: 0.6443 (tptt) REVERT: B 479 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6498 (ptt) REVERT: B 486 ILE cc_start: 0.6311 (mm) cc_final: 0.6098 (mm) REVERT: B 488 THR cc_start: 0.8499 (p) cc_final: 0.8246 (p) REVERT: B 518 GLN cc_start: 0.6111 (mp10) cc_final: 0.5423 (mp10) REVERT: C 201 VAL cc_start: 0.7427 (t) cc_final: 0.7148 (p) REVERT: C 227 GLN cc_start: 0.8103 (pp30) cc_final: 0.7622 (pt0) REVERT: C 256 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7337 (mt-10) REVERT: C 336 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6501 (mmm160) REVERT: C 517 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7018 (tm-30) REVERT: C 543 THR cc_start: 0.8724 (p) cc_final: 0.8445 (p) REVERT: D 248 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6722 (tpt90) REVERT: D 301 HIS cc_start: 0.7425 (p-80) cc_final: 0.7073 (p90) REVERT: D 379 ILE cc_start: 0.1719 (OUTLIER) cc_final: 0.1335 (tp) REVERT: D 394 MET cc_start: 0.4757 (mmt) cc_final: 0.4206 (mmt) REVERT: D 457 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7244 (mtm-85) REVERT: D 464 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4047 (tpt) REVERT: D 479 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.3279 (tmm) REVERT: D 513 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6613 (pt0) REVERT: D 517 GLU cc_start: 0.5790 (mm-30) cc_final: 0.4496 (tt0) REVERT: E 47 LYS cc_start: 0.8422 (mttm) cc_final: 0.8105 (mttt) REVERT: E 65 ILE cc_start: 0.8467 (pt) cc_final: 0.8213 (pt) REVERT: E 75 LYS cc_start: 0.8218 (ptpp) cc_final: 0.7691 (tptp) REVERT: E 84 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8726 (t) REVERT: F 29 CYS cc_start: 0.7938 (t) cc_final: 0.7620 (m) REVERT: F 32 GLN cc_start: 0.6968 (tp40) cc_final: 0.6690 (tt0) REVERT: F 42 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7314 (tmm160) REVERT: F 91 GLN cc_start: 0.8584 (pm20) cc_final: 0.8364 (pm20) outliers start: 178 outliers final: 26 residues processed: 575 average time/residue: 0.1702 time to fit residues: 131.0486 Evaluate side-chains 288 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 513 GLU Chi-restraints excluded: chain D residue 515 ARG Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 120 GLN B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN B 522 HIS C 310 GLN C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 451 HIS ** D 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.161399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115410 restraints weight = 28869.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.119509 restraints weight = 14365.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.122295 restraints weight = 9313.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.124049 restraints weight = 7085.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.125117 restraints weight = 5983.131| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15945 Z= 0.222 Angle : 1.068 55.005 21847 Z= 0.479 Chirality : 0.052 0.219 2361 Planarity : 0.008 0.121 2644 Dihedral : 18.584 137.564 2797 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 5.03 % Allowed : 14.43 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.19), residues: 1773 helix: -0.23 (0.17), residues: 837 sheet: -0.77 (0.46), residues: 120 loop : -2.21 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 369 TYR 0.028 0.003 TYR A 553 PHE 0.020 0.002 PHE A 153 TRP 0.037 0.003 TRP D 327 HIS 0.011 0.002 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (15941) covalent geometry : angle 0.90007 / 0.48 (21835) hydrogen bonds : bond 0.07538 / 4.81 ( 770) hydrogen bonds : angle 5.90646 / 4.24 ( 2169) metal coordination : bond 0.01658 / 1.03 ( 4) metal coordination : angle 24.56464 / 12.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 285 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8258 (ttm) cc_final: 0.7747 (ttm) REVERT: A 43 ASP cc_start: 0.8775 (t0) cc_final: 0.8468 (t0) REVERT: A 256 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7225 (tt0) REVERT: A 358 MET cc_start: 0.6364 (mmm) cc_final: 0.6130 (ppp) REVERT: A 524 ILE cc_start: 0.7486 (mp) cc_final: 0.7244 (mp) REVERT: A 526 LYS cc_start: 0.8164 (mttm) cc_final: 0.7953 (mptt) REVERT: B 389 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: C 227 GLN cc_start: 0.8412 (pp30) cc_final: 0.7792 (pt0) REVERT: C 259 GLN cc_start: 0.8466 (mt0) cc_final: 0.8189 (mt0) REVERT: C 265 ASN cc_start: 0.8143 (m-40) cc_final: 0.7665 (t0) REVERT: C 280 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7464 (pp20) REVERT: C 291 TRP cc_start: 0.7187 (t-100) cc_final: 0.6221 (t60) REVERT: C 334 ASN cc_start: 0.8628 (m-40) cc_final: 0.8302 (m110) REVERT: C 336 ARG cc_start: 0.7562 (mmp80) cc_final: 0.6547 (mmm160) REVERT: C 373 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7322 (mp) REVERT: C 418 PRO cc_start: 0.8471 (Cg_exo) cc_final: 0.8251 (Cg_endo) REVERT: C 479 MET cc_start: 0.8837 (mmt) cc_final: 0.8280 (mmm) REVERT: C 483 ASN cc_start: 0.8580 (m-40) cc_final: 0.8128 (m-40) REVERT: C 517 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6859 (tp30) REVERT: D 301 HIS cc_start: 0.7536 (p-80) cc_final: 0.6888 (p90) REVERT: D 302 ARG cc_start: 0.6303 (tpp-160) cc_final: 0.6039 (tpt90) REVERT: D 318 GLU cc_start: 0.5814 (pp20) cc_final: 0.5604 (mp0) REVERT: D 358 MET cc_start: 0.6755 (mpp) cc_final: 0.6513 (mpp) REVERT: D 379 ILE cc_start: 0.2164 (OUTLIER) cc_final: 0.1676 (tp) REVERT: D 394 MET cc_start: 0.5224 (mmt) cc_final: 0.4359 (mmt) REVERT: D 430 LEU cc_start: 0.5506 (mt) cc_final: 0.5000 (mp) REVERT: D 457 ARG cc_start: 0.7354 (mtm180) cc_final: 0.6961 (mtm-85) REVERT: E 47 LYS cc_start: 0.8964 (mttm) cc_final: 0.8494 (mttt) REVERT: E 54 GLU cc_start: 0.7346 (pp20) cc_final: 0.6766 (pp20) REVERT: E 61 ASP cc_start: 0.8356 (m-30) cc_final: 0.8006 (m-30) REVERT: E 75 LYS cc_start: 0.8397 (ptpp) cc_final: 0.8124 (tptp) REVERT: F 91 GLN cc_start: 0.8553 (pm20) cc_final: 0.8284 (pm20) outliers start: 75 outliers final: 34 residues processed: 332 average time/residue: 0.1291 time to fit residues: 62.0747 Evaluate side-chains 262 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 71 optimal weight: 0.2980 chunk 179 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 177 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 124 GLN A 420 ASN B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.156887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.113497 restraints weight = 29092.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115245 restraints weight = 16298.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117060 restraints weight = 10286.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117129 restraints weight = 8325.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117599 restraints weight = 7844.596| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15945 Z= 0.188 Angle : 0.902 41.519 21847 Z= 0.419 Chirality : 0.048 0.212 2361 Planarity : 0.006 0.120 2644 Dihedral : 17.435 136.758 2705 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.77 % Favored : 93.12 % Rotamer: Outliers : 3.49 % Allowed : 17.92 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 1773 helix: 0.34 (0.17), residues: 834 sheet: -1.10 (0.41), residues: 136 loop : -2.07 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 515 TYR 0.026 0.002 TYR A 21 PHE 0.027 0.002 PHE B 525 TRP 0.016 0.002 TRP B 327 HIS 0.007 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (15941) covalent geometry : angle 0.79207 / 0.42 (21835) hydrogen bonds : bond 0.06691 / 4.37 ( 770) hydrogen bonds : angle 5.32913 / 3.83 ( 2169) metal coordination : bond 0.01146 / 0.69 ( 4) metal coordination : angle 18.46500 / 9.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8757 (t0) cc_final: 0.8473 (t0) REVERT: A 120 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: A 232 TYR cc_start: 0.8424 (t80) cc_final: 0.7882 (t80) REVERT: A 256 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7240 (tt0) REVERT: A 349 GLU cc_start: 0.7141 (mp0) cc_final: 0.6885 (mp0) REVERT: A 351 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7466 (mmtt) REVERT: A 524 ILE cc_start: 0.7369 (mp) cc_final: 0.7050 (mt) REVERT: A 526 LYS cc_start: 0.8525 (mttm) cc_final: 0.8243 (mptt) REVERT: A 536 GLU cc_start: 0.7760 (tt0) cc_final: 0.7258 (mt-10) REVERT: B 394 MET cc_start: 0.8134 (tpp) cc_final: 0.7719 (mtt) REVERT: B 506 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8718 (mttt) REVERT: B 538 GLN cc_start: 0.8230 (mm110) cc_final: 0.7912 (mm-40) REVERT: B 555 ASN cc_start: 0.7151 (m110) cc_final: 0.6747 (m110) REVERT: C 227 GLN cc_start: 0.8559 (pp30) cc_final: 0.7885 (pt0) REVERT: C 265 ASN cc_start: 0.8134 (m-40) cc_final: 0.7614 (t0) REVERT: C 280 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: C 291 TRP cc_start: 0.7079 (t-100) cc_final: 0.6815 (t60) REVERT: C 336 ARG cc_start: 0.7631 (mmp80) cc_final: 0.6861 (mmm160) REVERT: C 373 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7333 (pp) REVERT: C 479 MET cc_start: 0.8903 (mmt) cc_final: 0.8435 (mmm) REVERT: C 483 ASN cc_start: 0.8658 (m-40) cc_final: 0.8294 (m-40) REVERT: C 517 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6786 (tp30) REVERT: D 301 HIS cc_start: 0.7488 (p-80) cc_final: 0.7062 (p90) REVERT: D 344 ARG cc_start: 0.6729 (mtp180) cc_final: 0.5062 (mpt180) REVERT: D 358 MET cc_start: 0.6592 (mpp) cc_final: 0.6379 (mpp) REVERT: D 379 ILE cc_start: 0.2846 (OUTLIER) cc_final: 0.2489 (tp) REVERT: D 394 MET cc_start: 0.4385 (mmt) cc_final: 0.3682 (mmt) REVERT: D 429 MET cc_start: 0.6029 (mmt) cc_final: 0.4729 (ptp) REVERT: D 430 LEU cc_start: 0.5607 (mt) cc_final: 0.5158 (mp) REVERT: D 479 MET cc_start: 0.3345 (mmt) cc_final: 0.1491 (tpt) REVERT: E 22 LYS cc_start: 0.8854 (pptt) cc_final: 0.8385 (pttm) REVERT: E 47 LYS cc_start: 0.9060 (mttm) cc_final: 0.8704 (mttt) REVERT: E 61 ASP cc_start: 0.8465 (m-30) cc_final: 0.8068 (m-30) REVERT: E 88 ILE cc_start: 0.8789 (mm) cc_final: 0.8530 (mt) REVERT: F 54 GLU cc_start: 0.7241 (pp20) cc_final: 0.7016 (pp20) REVERT: F 91 GLN cc_start: 0.8446 (pm20) cc_final: 0.8179 (pm20) outliers start: 52 outliers final: 29 residues processed: 282 average time/residue: 0.1292 time to fit residues: 52.3719 Evaluate side-chains 242 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 420 ASN B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107858 restraints weight = 29070.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110017 restraints weight = 16262.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112449 restraints weight = 10011.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112704 restraints weight = 8223.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112793 restraints weight = 7324.604| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15945 Z= 0.201 Angle : 0.799 29.869 21847 Z= 0.396 Chirality : 0.047 0.211 2361 Planarity : 0.006 0.121 2644 Dihedral : 17.324 135.966 2702 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.69 % Allowed : 18.99 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.19), residues: 1773 helix: 0.60 (0.17), residues: 844 sheet: -0.73 (0.41), residues: 146 loop : -2.01 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 540 TYR 0.025 0.002 TYR D 527 PHE 0.019 0.002 PHE B 407 TRP 0.015 0.002 TRP F 17 HIS 0.009 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (15941) covalent geometry : angle 0.73746 / 0.39 (21835) hydrogen bonds : bond 0.06547 / 4.25 ( 770) hydrogen bonds : angle 5.07334 / 3.63 ( 2169) metal coordination : bond 0.00993 / 0.62 ( 4) metal coordination : angle 13.17420 / 7.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.8445 (t80) cc_final: 0.8103 (t80) REVERT: A 256 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7366 (tt0) REVERT: A 349 GLU cc_start: 0.7247 (mp0) cc_final: 0.6880 (mp0) REVERT: A 358 MET cc_start: 0.7308 (mmp) cc_final: 0.6334 (ppp) REVERT: A 429 MET cc_start: 0.8676 (tmm) cc_final: 0.8035 (tmm) REVERT: A 464 MET cc_start: 0.9134 (tpp) cc_final: 0.8826 (tpt) REVERT: A 479 MET cc_start: 0.7350 (ttm) cc_final: 0.6980 (ttm) REVERT: A 526 LYS cc_start: 0.8573 (mttm) cc_final: 0.8206 (mptt) REVERT: B 387 TYR cc_start: 0.7421 (t80) cc_final: 0.7194 (t80) REVERT: B 389 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7745 (mm110) REVERT: B 394 MET cc_start: 0.8030 (tpp) cc_final: 0.7806 (mtt) REVERT: B 506 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8656 (mttm) REVERT: B 555 ASN cc_start: 0.7174 (m110) cc_final: 0.6820 (m110) REVERT: C 227 GLN cc_start: 0.8486 (pp30) cc_final: 0.7895 (pt0) REVERT: C 280 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7827 (pp20) REVERT: C 291 TRP cc_start: 0.7406 (t-100) cc_final: 0.6509 (t60) REVERT: C 336 ARG cc_start: 0.7787 (mmp80) cc_final: 0.7353 (mtp85) REVERT: C 373 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7283 (pp) REVERT: C 389 GLN cc_start: 0.7470 (mp10) cc_final: 0.7015 (mp10) REVERT: C 465 MET cc_start: 0.8161 (ttm) cc_final: 0.7436 (tpt) REVERT: C 479 MET cc_start: 0.8932 (mmt) cc_final: 0.8441 (mmm) REVERT: C 483 ASN cc_start: 0.8689 (m-40) cc_final: 0.8327 (m-40) REVERT: C 500 LEU cc_start: 0.7234 (mm) cc_final: 0.6933 (mm) REVERT: C 517 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6868 (tp30) REVERT: C 535 LEU cc_start: 0.6851 (mt) cc_final: 0.6496 (mt) REVERT: D 301 HIS cc_start: 0.7568 (p-80) cc_final: 0.7215 (p90) REVERT: D 344 ARG cc_start: 0.6718 (mtp180) cc_final: 0.4985 (mpt90) REVERT: D 379 ILE cc_start: 0.2892 (OUTLIER) cc_final: 0.2578 (tp) REVERT: D 394 MET cc_start: 0.4577 (mmt) cc_final: 0.3987 (mmt) REVERT: D 429 MET cc_start: 0.5975 (mmt) cc_final: 0.4296 (ptp) REVERT: D 430 LEU cc_start: 0.5711 (mt) cc_final: 0.5295 (mp) REVERT: E 9 TYR cc_start: 0.8428 (p90) cc_final: 0.8149 (p90) REVERT: E 22 LYS cc_start: 0.9017 (pptt) cc_final: 0.8652 (pttm) REVERT: E 61 ASP cc_start: 0.8580 (m-30) cc_final: 0.8216 (m-30) REVERT: E 65 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8729 (mt) REVERT: F 10 ASP cc_start: 0.7962 (m-30) cc_final: 0.7741 (m-30) REVERT: F 91 GLN cc_start: 0.8442 (pm20) cc_final: 0.7997 (pm20) outliers start: 55 outliers final: 29 residues processed: 253 average time/residue: 0.1266 time to fit residues: 46.7067 Evaluate side-chains 236 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 138 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.151205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108545 restraints weight = 28263.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109454 restraints weight = 15716.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111051 restraints weight = 10052.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111586 restraints weight = 8057.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111711 restraints weight = 7438.644| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15945 Z= 0.187 Angle : 0.775 23.667 21847 Z= 0.383 Chirality : 0.046 0.189 2361 Planarity : 0.006 0.118 2644 Dihedral : 17.281 136.114 2698 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.37 % Favored : 93.57 % Rotamer: Outliers : 3.69 % Allowed : 19.80 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.19), residues: 1773 helix: 0.84 (0.18), residues: 832 sheet: -0.57 (0.41), residues: 149 loop : -1.98 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 544 TYR 0.020 0.002 TYR D 527 PHE 0.016 0.001 PHE C 407 TRP 0.018 0.002 TRP D 327 HIS 0.005 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (15941) covalent geometry : angle 0.73290 / 0.38 (21835) hydrogen bonds : bond 0.06460 / 4.19 ( 770) hydrogen bonds : angle 4.94549 / 3.52 ( 2169) metal coordination : bond 0.00838 / 0.51 ( 4) metal coordination : angle 10.82930 / 6.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.8078 (t70) cc_final: 0.7710 (t70) REVERT: A 115 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: A 140 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8350 (mp) REVERT: A 232 TYR cc_start: 0.8482 (t80) cc_final: 0.8263 (t80) REVERT: A 256 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7334 (tt0) REVERT: A 429 MET cc_start: 0.8591 (tmm) cc_final: 0.8123 (tmm) REVERT: A 464 MET cc_start: 0.9148 (tpp) cc_final: 0.8912 (tpt) REVERT: A 479 MET cc_start: 0.7381 (ttm) cc_final: 0.7059 (ttm) REVERT: A 526 LYS cc_start: 0.8621 (mttm) cc_final: 0.8275 (mptt) REVERT: B 413 ARG cc_start: 0.8649 (tpp-160) cc_final: 0.8345 (tpp80) REVERT: B 481 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8560 (mp) REVERT: C 227 GLN cc_start: 0.8517 (pp30) cc_final: 0.7911 (pt0) REVERT: C 280 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7869 (pp20) REVERT: C 291 TRP cc_start: 0.7163 (t-100) cc_final: 0.6682 (t60) REVERT: C 336 ARG cc_start: 0.7701 (mmp80) cc_final: 0.6928 (ttm-80) REVERT: C 373 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7255 (pp) REVERT: C 479 MET cc_start: 0.8960 (mmt) cc_final: 0.8403 (mmm) REVERT: C 483 ASN cc_start: 0.8698 (m-40) cc_final: 0.8300 (m-40) REVERT: C 500 LEU cc_start: 0.7282 (mm) cc_final: 0.7014 (mm) REVERT: D 344 ARG cc_start: 0.6604 (mtp180) cc_final: 0.4868 (mpt90) REVERT: D 379 ILE cc_start: 0.2836 (OUTLIER) cc_final: 0.2521 (tp) REVERT: D 394 MET cc_start: 0.4312 (mmt) cc_final: 0.3148 (mmt) REVERT: D 429 MET cc_start: 0.5625 (mmt) cc_final: 0.4368 (ptp) REVERT: D 451 HIS cc_start: 0.3814 (OUTLIER) cc_final: 0.2463 (m-70) REVERT: D 478 LEU cc_start: 0.4736 (pp) cc_final: 0.4444 (tp) REVERT: E 22 LYS cc_start: 0.8998 (pptt) cc_final: 0.8745 (pttt) REVERT: E 61 ASP cc_start: 0.8645 (m-30) cc_final: 0.8258 (m-30) REVERT: F 10 ASP cc_start: 0.8068 (m-30) cc_final: 0.7867 (m-30) REVERT: F 75 LYS cc_start: 0.7471 (mtmm) cc_final: 0.7200 (mmmt) REVERT: F 91 GLN cc_start: 0.8432 (pm20) cc_final: 0.7971 (pm20) outliers start: 55 outliers final: 30 residues processed: 253 average time/residue: 0.1306 time to fit residues: 47.8423 Evaluate side-chains 226 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 135 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.148014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104984 restraints weight = 28200.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105747 restraints weight = 15494.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107176 restraints weight = 10115.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107901 restraints weight = 8211.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108075 restraints weight = 7607.502| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15945 Z= 0.205 Angle : 0.764 16.687 21847 Z= 0.392 Chirality : 0.047 0.209 2361 Planarity : 0.006 0.117 2644 Dihedral : 17.118 135.988 2695 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.42 % Allowed : 19.87 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1773 helix: 0.89 (0.18), residues: 832 sheet: -0.88 (0.40), residues: 165 loop : -1.91 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 336 TYR 0.027 0.002 TYR C 527 PHE 0.015 0.002 PHE B 407 TRP 0.021 0.002 TRP D 327 HIS 0.007 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (15941) covalent geometry : angle 0.73940 / 0.39 (21835) hydrogen bonds : bond 0.06436 / 4.20 ( 770) hydrogen bonds : angle 4.90287 / 3.47 ( 2169) metal coordination : bond 0.00788 / 0.49 ( 4) metal coordination : angle 8.22116 / 5.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9256 (mp) cc_final: 0.9029 (mp) REVERT: A 105 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7858 (mtmm) REVERT: A 115 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: A 256 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7369 (tt0) REVERT: A 429 MET cc_start: 0.8704 (tmm) cc_final: 0.8409 (tmm) REVERT: A 479 MET cc_start: 0.7420 (ttm) cc_final: 0.7100 (ttm) REVERT: B 351 LYS cc_start: 0.7550 (tptt) cc_final: 0.7196 (tptt) REVERT: B 481 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8634 (mp) REVERT: C 227 GLN cc_start: 0.8693 (pp30) cc_final: 0.8050 (pt0) REVERT: C 291 TRP cc_start: 0.7339 (t-100) cc_final: 0.6883 (t60) REVERT: C 336 ARG cc_start: 0.7539 (mmp80) cc_final: 0.7099 (mtp85) REVERT: C 373 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7346 (pp) REVERT: C 517 GLU cc_start: 0.8257 (tm-30) cc_final: 0.8025 (tp30) REVERT: C 518 GLN cc_start: 0.7251 (tp-100) cc_final: 0.7015 (tp40) REVERT: D 301 HIS cc_start: 0.7711 (p-80) cc_final: 0.7064 (p90) REVERT: D 358 MET cc_start: 0.6485 (mpt) cc_final: 0.5704 (ttt) REVERT: D 394 MET cc_start: 0.4098 (mmt) cc_final: 0.3218 (mmt) REVERT: D 429 MET cc_start: 0.5782 (mmt) cc_final: 0.4512 (ptp) REVERT: D 451 HIS cc_start: 0.3991 (OUTLIER) cc_final: 0.2600 (m-70) REVERT: D 455 PHE cc_start: 0.4709 (m-80) cc_final: 0.4381 (m-80) REVERT: E 2 GLU cc_start: 0.8044 (tt0) cc_final: 0.7810 (tm-30) REVERT: E 61 ASP cc_start: 0.8643 (m-30) cc_final: 0.8220 (m-30) REVERT: F 1 MET cc_start: 0.7531 (tpp) cc_final: 0.7144 (tpp) REVERT: F 91 GLN cc_start: 0.8514 (pm20) cc_final: 0.8024 (pm20) outliers start: 51 outliers final: 33 residues processed: 233 average time/residue: 0.1367 time to fit residues: 45.3692 Evaluate side-chains 208 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 54 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 chunk 115 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 17 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.150568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101499 restraints weight = 28814.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.105055 restraints weight = 14585.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107461 restraints weight = 9750.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108846 restraints weight = 7605.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109842 restraints weight = 6598.954| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15945 Z= 0.146 Angle : 0.716 12.311 21847 Z= 0.367 Chirality : 0.044 0.195 2361 Planarity : 0.005 0.114 2644 Dihedral : 16.850 136.566 2690 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 3.36 % Allowed : 20.27 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1773 helix: 1.07 (0.18), residues: 839 sheet: -0.79 (0.40), residues: 166 loop : -1.87 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 336 TYR 0.017 0.001 TYR A 21 PHE 0.013 0.001 PHE B 512 TRP 0.018 0.002 TRP D 327 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (15941) covalent geometry : angle 0.69598 / 0.37 (21835) hydrogen bonds : bond 0.05981 / 3.87 ( 770) hydrogen bonds : angle 4.73438 / 3.35 ( 2169) metal coordination : bond 0.00391 / 0.23 ( 4) metal coordination : angle 7.18036 / 4.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9260 (mp) cc_final: 0.9045 (mp) REVERT: A 105 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7862 (mtmm) REVERT: A 256 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7259 (tt0) REVERT: A 351 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7312 (mmtt) REVERT: A 479 MET cc_start: 0.7437 (ttm) cc_final: 0.7149 (ttm) REVERT: B 479 MET cc_start: 0.8045 (mmt) cc_final: 0.7709 (mmm) REVERT: B 481 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8624 (mp) REVERT: C 227 GLN cc_start: 0.8650 (pp30) cc_final: 0.7997 (pt0) REVERT: C 291 TRP cc_start: 0.7140 (t-100) cc_final: 0.6649 (t60) REVERT: C 334 ASN cc_start: 0.8825 (m-40) cc_final: 0.8416 (m110) REVERT: C 336 ARG cc_start: 0.7531 (mmp80) cc_final: 0.7056 (ttm-80) REVERT: C 373 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7373 (pp) REVERT: C 465 MET cc_start: 0.7452 (ttm) cc_final: 0.6953 (ttm) REVERT: C 517 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8062 (tp30) REVERT: C 518 GLN cc_start: 0.7037 (tp-100) cc_final: 0.6718 (tp40) REVERT: D 301 HIS cc_start: 0.7751 (p-80) cc_final: 0.7337 (p90) REVERT: D 358 MET cc_start: 0.5953 (mpt) cc_final: 0.5398 (ttp) REVERT: D 362 ASP cc_start: 0.7802 (m-30) cc_final: 0.7552 (t70) REVERT: D 394 MET cc_start: 0.4667 (mmt) cc_final: 0.3405 (mmt) REVERT: D 429 MET cc_start: 0.5347 (mmt) cc_final: 0.4171 (ptp) REVERT: D 451 HIS cc_start: 0.3506 (OUTLIER) cc_final: 0.2446 (m-70) REVERT: D 479 MET cc_start: 0.1791 (mmt) cc_final: 0.1522 (mmt) REVERT: E 2 GLU cc_start: 0.7905 (tt0) cc_final: 0.7554 (tt0) REVERT: E 39 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8435 (ttt-90) REVERT: E 61 ASP cc_start: 0.8514 (m-30) cc_final: 0.8123 (m-30) REVERT: F 1 MET cc_start: 0.7446 (tpp) cc_final: 0.7193 (tpp) REVERT: F 49 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7529 (mt-10) REVERT: F 91 GLN cc_start: 0.8516 (pm20) cc_final: 0.8089 (pm20) outliers start: 50 outliers final: 29 residues processed: 239 average time/residue: 0.1307 time to fit residues: 45.1938 Evaluate side-chains 226 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 21 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 143 optimal weight: 30.0000 chunk 28 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 HIS A 227 GLN B 361 GLN C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.150927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.108004 restraints weight = 29003.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108237 restraints weight = 16354.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109241 restraints weight = 11279.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109659 restraints weight = 9325.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109914 restraints weight = 8583.168| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15945 Z= 0.146 Angle : 0.702 12.441 21847 Z= 0.360 Chirality : 0.045 0.231 2361 Planarity : 0.006 0.114 2644 Dihedral : 16.778 137.582 2688 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.95 % Allowed : 20.87 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1773 helix: 1.16 (0.18), residues: 838 sheet: -0.93 (0.38), residues: 180 loop : -1.86 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 336 TYR 0.016 0.001 TYR B 545 PHE 0.011 0.001 PHE B 512 TRP 0.018 0.001 TRP D 327 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (15941) covalent geometry : angle 0.68360 / 0.36 (21835) hydrogen bonds : bond 0.05867 / 3.78 ( 770) hydrogen bonds : angle 4.67321 / 3.30 ( 2169) metal coordination : bond 0.00371 / 0.22 ( 4) metal coordination : angle 6.87744 / 4.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9231 (mp) cc_final: 0.9004 (mp) REVERT: A 43 ASP cc_start: 0.8804 (t0) cc_final: 0.8530 (t0) REVERT: A 105 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7837 (mtmm) REVERT: A 227 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7183 (pp30) REVERT: A 256 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7275 (tt0) REVERT: A 358 MET cc_start: 0.7540 (mmp) cc_final: 0.6066 (tmm) REVERT: A 429 MET cc_start: 0.8603 (tmm) cc_final: 0.8217 (tmm) REVERT: A 479 MET cc_start: 0.7466 (ttm) cc_final: 0.7035 (ttm) REVERT: B 227 GLN cc_start: 0.7522 (mp10) cc_final: 0.7312 (mp10) REVERT: B 351 LYS cc_start: 0.7342 (tptt) cc_final: 0.6893 (tptt) REVERT: B 479 MET cc_start: 0.8025 (mmt) cc_final: 0.7540 (mmm) REVERT: B 481 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8621 (mp) REVERT: C 227 GLN cc_start: 0.8661 (pp30) cc_final: 0.8023 (pt0) REVERT: C 291 TRP cc_start: 0.7228 (t-100) cc_final: 0.6750 (t60) REVERT: C 334 ASN cc_start: 0.8826 (m-40) cc_final: 0.8419 (m110) REVERT: C 465 MET cc_start: 0.7324 (ttm) cc_final: 0.6909 (ttm) REVERT: C 500 LEU cc_start: 0.7579 (mm) cc_final: 0.7372 (mm) REVERT: C 518 GLN cc_start: 0.7039 (tp-100) cc_final: 0.6748 (tp40) REVERT: C 536 GLU cc_start: 0.8709 (pm20) cc_final: 0.8334 (pm20) REVERT: D 230 LYS cc_start: 0.5416 (OUTLIER) cc_final: 0.4197 (tppt) REVERT: D 301 HIS cc_start: 0.7714 (p-80) cc_final: 0.7306 (p90) REVERT: D 321 LEU cc_start: 0.5553 (mm) cc_final: 0.5273 (mt) REVERT: D 358 MET cc_start: 0.6110 (mpt) cc_final: 0.5224 (ttp) REVERT: D 362 ASP cc_start: 0.7826 (m-30) cc_final: 0.7486 (t70) REVERT: D 394 MET cc_start: 0.3778 (mmt) cc_final: 0.3117 (mmt) REVERT: D 429 MET cc_start: 0.5606 (mmt) cc_final: 0.4636 (mtm) REVERT: D 451 HIS cc_start: 0.3684 (OUTLIER) cc_final: 0.2439 (m-70) REVERT: E 2 GLU cc_start: 0.7859 (tt0) cc_final: 0.7572 (tt0) REVERT: E 39 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8415 (ttt-90) REVERT: E 61 ASP cc_start: 0.8493 (m-30) cc_final: 0.8098 (m-30) REVERT: F 1 MET cc_start: 0.7474 (tpp) cc_final: 0.7164 (tpp) REVERT: F 49 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7510 (mt-10) REVERT: F 91 GLN cc_start: 0.8533 (pm20) cc_final: 0.8100 (pm20) outliers start: 44 outliers final: 30 residues processed: 226 average time/residue: 0.1213 time to fit residues: 40.3005 Evaluate side-chains 220 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.150271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106512 restraints weight = 28802.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108536 restraints weight = 15466.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109519 restraints weight = 10015.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109905 restraints weight = 8527.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110316 restraints weight = 7811.130| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15945 Z= 0.155 Angle : 0.711 12.375 21847 Z= 0.365 Chirality : 0.045 0.426 2361 Planarity : 0.005 0.112 2644 Dihedral : 16.748 137.729 2686 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 2.89 % Allowed : 21.28 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1773 helix: 1.20 (0.18), residues: 839 sheet: -0.95 (0.38), residues: 183 loop : -1.86 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 336 TYR 0.014 0.001 TYR D 527 PHE 0.014 0.001 PHE B 407 TRP 0.020 0.001 TRP D 327 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (15941) covalent geometry : angle 0.69312 / 0.36 (21835) hydrogen bonds : bond 0.05858 / 3.78 ( 770) hydrogen bonds : angle 4.63551 / 3.28 ( 2169) metal coordination : bond 0.00425 / 0.25 ( 4) metal coordination : angle 6.71387 / 4.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9243 (mp) cc_final: 0.9024 (mp) REVERT: A 43 ASP cc_start: 0.8813 (t0) cc_final: 0.8558 (t0) REVERT: A 105 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7807 (mtmm) REVERT: A 256 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7282 (tt0) REVERT: A 351 LYS cc_start: 0.7636 (mmmt) cc_final: 0.7213 (mmtt) REVERT: A 358 MET cc_start: 0.7564 (mmp) cc_final: 0.6130 (tmm) REVERT: A 429 MET cc_start: 0.8660 (tmm) cc_final: 0.8260 (tmm) REVERT: A 479 MET cc_start: 0.7473 (ttm) cc_final: 0.7051 (ttm) REVERT: A 526 LYS cc_start: 0.8734 (mttm) cc_final: 0.8350 (pttm) REVERT: B 227 GLN cc_start: 0.7595 (mp10) cc_final: 0.7354 (mp10) REVERT: B 351 LYS cc_start: 0.7451 (tptt) cc_final: 0.6932 (tptt) REVERT: B 479 MET cc_start: 0.7902 (mmt) cc_final: 0.7565 (mmm) REVERT: B 481 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8645 (mp) REVERT: C 227 GLN cc_start: 0.8630 (pp30) cc_final: 0.8007 (pt0) REVERT: C 291 TRP cc_start: 0.7246 (t-100) cc_final: 0.6783 (t60) REVERT: C 334 ASN cc_start: 0.8811 (m-40) cc_final: 0.8434 (m110) REVERT: C 361 GLN cc_start: 0.9115 (mm110) cc_final: 0.8818 (mm110) REVERT: C 465 MET cc_start: 0.7309 (ttm) cc_final: 0.6924 (ttm) REVERT: C 500 LEU cc_start: 0.7507 (mm) cc_final: 0.6974 (mm) REVERT: C 518 GLN cc_start: 0.7153 (tp-100) cc_final: 0.6937 (tp40) REVERT: C 536 GLU cc_start: 0.8687 (pm20) cc_final: 0.8348 (pm20) REVERT: D 230 LYS cc_start: 0.5406 (OUTLIER) cc_final: 0.4175 (tppt) REVERT: D 301 HIS cc_start: 0.7868 (p-80) cc_final: 0.7485 (p90) REVERT: D 358 MET cc_start: 0.6033 (mpt) cc_final: 0.5220 (ttp) REVERT: D 362 ASP cc_start: 0.7833 (m-30) cc_final: 0.7493 (t70) REVERT: D 429 MET cc_start: 0.6042 (mmt) cc_final: 0.4999 (ptp) REVERT: D 434 TRP cc_start: 0.6897 (m100) cc_final: 0.6523 (m100) REVERT: D 451 HIS cc_start: 0.3529 (OUTLIER) cc_final: 0.2527 (m-70) REVERT: E 2 GLU cc_start: 0.7809 (tt0) cc_final: 0.7586 (tt0) REVERT: E 39 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8435 (ttt-90) REVERT: E 61 ASP cc_start: 0.8484 (m-30) cc_final: 0.8115 (m-30) REVERT: F 91 GLN cc_start: 0.8566 (pm20) cc_final: 0.8116 (pm20) outliers start: 43 outliers final: 33 residues processed: 217 average time/residue: 0.1252 time to fit residues: 39.8814 Evaluate side-chains 218 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 124 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.150103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105855 restraints weight = 28871.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106565 restraints weight = 16185.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107927 restraints weight = 10606.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108345 restraints weight = 8949.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108473 restraints weight = 8275.754| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15945 Z= 0.149 Angle : 0.711 12.561 21847 Z= 0.363 Chirality : 0.045 0.354 2361 Planarity : 0.005 0.111 2644 Dihedral : 16.734 137.635 2686 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.75 % Allowed : 21.54 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1773 helix: 1.21 (0.18), residues: 844 sheet: -0.93 (0.38), residues: 183 loop : -1.86 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 336 TYR 0.015 0.001 TYR B 387 PHE 0.014 0.001 PHE B 407 TRP 0.021 0.002 TRP D 327 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (15941) covalent geometry : angle 0.69431 / 0.36 (21835) hydrogen bonds : bond 0.05825 / 3.74 ( 770) hydrogen bonds : angle 4.59450 / 3.25 ( 2169) metal coordination : bond 0.00395 / 0.23 ( 4) metal coordination : angle 6.60228 / 4.70 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9244 (mp) cc_final: 0.9023 (mp) REVERT: A 43 ASP cc_start: 0.8815 (t0) cc_final: 0.8558 (t0) REVERT: A 105 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7787 (mtmm) REVERT: A 256 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7272 (tt0) REVERT: A 358 MET cc_start: 0.7574 (mmp) cc_final: 0.6130 (tmm) REVERT: A 429 MET cc_start: 0.8681 (tmm) cc_final: 0.8301 (tmm) REVERT: A 479 MET cc_start: 0.7543 (ttm) cc_final: 0.7155 (ttm) REVERT: A 526 LYS cc_start: 0.8761 (mttm) cc_final: 0.8357 (pttm) REVERT: B 227 GLN cc_start: 0.7615 (mp10) cc_final: 0.7394 (mp10) REVERT: B 351 LYS cc_start: 0.7487 (tptt) cc_final: 0.6957 (tptt) REVERT: B 481 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8644 (mp) REVERT: C 220 ARG cc_start: 0.6225 (ppt170) cc_final: 0.6022 (ppt170) REVERT: C 227 GLN cc_start: 0.8654 (pp30) cc_final: 0.8014 (pt0) REVERT: C 291 TRP cc_start: 0.7210 (t-100) cc_final: 0.6741 (t60) REVERT: C 334 ASN cc_start: 0.8809 (m-40) cc_final: 0.8430 (m110) REVERT: C 358 MET cc_start: 0.8676 (ppp) cc_final: 0.8271 (ppp) REVERT: C 361 GLN cc_start: 0.9053 (mm110) cc_final: 0.8805 (mm110) REVERT: C 500 LEU cc_start: 0.7509 (mm) cc_final: 0.6964 (mm) REVERT: C 518 GLN cc_start: 0.7075 (tp-100) cc_final: 0.6831 (tp40) REVERT: C 536 GLU cc_start: 0.8687 (pm20) cc_final: 0.8381 (pm20) REVERT: D 230 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.3943 (tppt) REVERT: D 301 HIS cc_start: 0.7707 (p-80) cc_final: 0.6952 (p90) REVERT: D 358 MET cc_start: 0.5957 (mpt) cc_final: 0.5263 (ttp) REVERT: D 362 ASP cc_start: 0.7809 (m-30) cc_final: 0.7513 (t70) REVERT: D 429 MET cc_start: 0.5988 (mmt) cc_final: 0.4952 (ptp) REVERT: D 430 LEU cc_start: 0.6756 (mm) cc_final: 0.6478 (mm) REVERT: D 451 HIS cc_start: 0.3325 (OUTLIER) cc_final: 0.2417 (m-70) REVERT: E 39 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8435 (ttt-90) REVERT: E 61 ASP cc_start: 0.8477 (m-30) cc_final: 0.8120 (m-30) REVERT: F 91 GLN cc_start: 0.8577 (pm20) cc_final: 0.8118 (pm20) outliers start: 41 outliers final: 31 residues processed: 216 average time/residue: 0.1201 time to fit residues: 38.3160 Evaluate side-chains 214 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 77 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.149957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105848 restraints weight = 28789.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106525 restraints weight = 16037.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107886 restraints weight = 10530.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.108207 restraints weight = 8954.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108490 restraints weight = 8199.960| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15945 Z= 0.147 Angle : 0.707 12.728 21847 Z= 0.361 Chirality : 0.045 0.305 2361 Planarity : 0.005 0.110 2644 Dihedral : 16.724 137.519 2686 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.55 % Allowed : 21.95 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1773 helix: 1.28 (0.18), residues: 838 sheet: -0.94 (0.38), residues: 183 loop : -1.81 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 386 TYR 0.015 0.001 TYR B 387 PHE 0.014 0.001 PHE B 407 TRP 0.037 0.002 TRP D 434 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (15941) covalent geometry : angle 0.69079 / 0.36 (21835) hydrogen bonds : bond 0.05782 / 3.71 ( 770) hydrogen bonds : angle 4.56983 / 3.24 ( 2169) metal coordination : bond 0.00387 / 0.23 ( 4) metal coordination : angle 6.47607 / 4.67 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.54 seconds wall clock time: 46 minutes 40.15 seconds (2800.15 seconds total)