Starting phenix.real_space_refine on Wed Mar 4 18:32:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi5_23840/03_2026/7mi5_23840_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi5_23840/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mi5_23840/03_2026/7mi5_23840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi5_23840/03_2026/7mi5_23840.map" model { file = "/net/cci-nas-00/data/ceres_data/7mi5_23840/03_2026/7mi5_23840_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi5_23840/03_2026/7mi5_23840_neut.cif" } 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-dev-5986/lib/python3.9/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: 4.05, 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: 1.62 Conformation dependent library (CDL) restraints added in 511.4 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: 1.95 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: 2.77 Time building geometry restraints manager: 2.05 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 1.460 1.360 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1' DA H 21 " pdb=" N9 DA H 21 " ideal model delta sigma weight residual 1.460 1.368 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" SD MET D 364 " pdb=" CE MET D 364 " ideal model delta sigma weight residual 1.791 1.695 0.096 2.50e-02 1.60e+03 1.46e+01 bond pdb=" SD MET B 364 " pdb=" CE MET B 364 " ideal model delta sigma weight residual 1.791 1.696 0.095 2.50e-02 1.60e+03 1.44e+01 bond pdb=" C LEU A 197 " pdb=" O LEU A 197 " ideal model delta sigma weight residual 1.233 1.250 -0.017 4.80e-03 4.34e+04 1.29e+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: 2013 0.084 - 0.169: 293 0.169 - 0.253: 47 0.253 - 0.338: 6 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: 0.640 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.820 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 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= 0.471 Angle : 1.605 60.520 21847 Z= 0.789 Chirality : 0.063 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 covalent geometry : bond 0.00970 (15941) covalent geometry : angle 1.46804 (21835) hydrogen bonds : bond 0.17744 ( 770) hydrogen bonds : angle 8.00788 ( 2169) metal coordination : bond 0.18912 ( 4) metal coordination : angle 27.70161 ( 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 : 0.532 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: 0.6933 (t) REVERT: A 154 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.5556 (t70) REVERT: A 256 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7269 (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: 0.5422 (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: 0.1336 (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: 0.6689 (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: 0.1777 time to fit residues: 135.7702 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 : 0.478 ------------------------------------------------------------------------------- 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: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 5.9990 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: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.160702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.113880 restraints weight = 28799.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117977 restraints weight = 14465.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120700 restraints weight = 9437.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.122417 restraints weight = 7254.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123466 restraints weight = 6126.603| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4008 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= 0.201 Angle : 0.979 47.747 21847 Z= 0.445 Chirality : 0.049 0.221 2361 Planarity : 0.007 0.128 2644 Dihedral : 18.469 139.316 2797 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.82 % Favored : 93.06 % Rotamer: Outliers : 4.56 % Allowed : 14.03 % Favored : 81.41 % 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: -1.42 (0.19), residues: 1773 helix: 0.07 (0.17), residues: 838 sheet: -0.58 (0.47), residues: 120 loop : -2.11 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 336 TYR 0.029 0.002 TYR A 553 PHE 0.024 0.002 PHE B 425 TRP 0.033 0.002 TRP D 327 HIS 0.011 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00453 (15941) covalent geometry : angle 0.84173 (21835) hydrogen bonds : bond 0.06668 ( 770) hydrogen bonds : angle 5.54722 ( 2169) metal coordination : bond 0.01361 ( 4) metal coordination : angle 21.37531 ( 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 359 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 291 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8985 (t80) cc_final: 0.8726 (t80) REVERT: A 43 ASP cc_start: 0.8736 (t0) cc_final: 0.8504 (t0) REVERT: A 90 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6648 (pt0) REVERT: A 256 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7279 (tt0) REVERT: A 280 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: A 524 ILE cc_start: 0.7455 (mp) cc_final: 0.7221 (mp) REVERT: A 526 LYS cc_start: 0.8264 (mttm) cc_final: 0.8058 (mptt) REVERT: B 389 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: B 506 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8614 (mtmm) REVERT: B 518 GLN cc_start: 0.7253 (mp10) cc_final: 0.7016 (mp10) REVERT: B 538 GLN cc_start: 0.8325 (mm110) cc_final: 0.7924 (mm-40) REVERT: B 542 LEU cc_start: 0.8289 (tp) cc_final: 0.8056 (tt) REVERT: B 555 ASN cc_start: 0.7090 (m110) cc_final: 0.6866 (m110) REVERT: C 227 GLN cc_start: 0.8424 (pp30) cc_final: 0.7738 (pt0) REVERT: C 236 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6980 (p0) REVERT: C 259 GLN cc_start: 0.8551 (mt0) cc_final: 0.8249 (mt0) REVERT: C 265 ASN cc_start: 0.8053 (m-40) cc_final: 0.7593 (t0) REVERT: C 280 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: C 291 TRP cc_start: 0.7205 (t-100) cc_final: 0.6231 (t60) REVERT: C 336 ARG cc_start: 0.7633 (mmp80) cc_final: 0.6898 (mmm160) REVERT: C 373 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7300 (mp) REVERT: C 418 PRO cc_start: 0.8533 (Cg_exo) cc_final: 0.8310 (Cg_endo) REVERT: C 479 MET cc_start: 0.8867 (mmt) cc_final: 0.8385 (mmm) REVERT: C 483 ASN cc_start: 0.8633 (m-40) cc_final: 0.8218 (m110) REVERT: C 517 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6813 (tp30) REVERT: D 301 HIS cc_start: 0.7455 (p-80) cc_final: 0.6810 (p90) REVERT: D 344 ARG cc_start: 0.6882 (mtp180) cc_final: 0.5310 (mpt90) REVERT: D 379 ILE cc_start: 0.2818 (OUTLIER) cc_final: 0.2383 (tp) REVERT: D 430 LEU cc_start: 0.5635 (mt) cc_final: 0.5255 (mp) REVERT: D 479 MET cc_start: 0.3838 (mtm) cc_final: 0.2237 (tpt) REVERT: E 47 LYS cc_start: 0.9027 (mttm) cc_final: 0.8527 (mttt) REVERT: E 61 ASP cc_start: 0.8425 (m-30) cc_final: 0.8114 (m-30) REVERT: E 75 LYS cc_start: 0.8340 (ptpp) cc_final: 0.8108 (tptp) REVERT: F 91 GLN cc_start: 0.8449 (pm20) cc_final: 0.8168 (pm20) outliers start: 68 outliers final: 29 residues processed: 333 average time/residue: 0.1433 time to fit residues: 67.2690 Evaluate side-chains 251 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 476 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 268 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 431 THR 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 236 ASP 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 373 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 71 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 150 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 411 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.154425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110658 restraints weight = 29217.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111282 restraints weight = 15955.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112973 restraints weight = 11063.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113583 restraints weight = 8874.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113803 restraints weight = 8045.207| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15945 Z= 0.183 Angle : 0.798 28.068 21847 Z= 0.388 Chirality : 0.046 0.172 2361 Planarity : 0.006 0.109 2644 Dihedral : 17.262 139.918 2704 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.56 % Allowed : 17.11 % Favored : 79.33 % 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: -0.91 (0.19), residues: 1773 helix: 0.68 (0.17), residues: 838 sheet: -0.61 (0.42), residues: 139 loop : -2.06 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 514 TYR 0.020 0.002 TYR A 21 PHE 0.025 0.002 PHE A 153 TRP 0.017 0.002 TRP B 327 HIS 0.008 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00417 (15941) covalent geometry : angle 0.74411 (21835) hydrogen bonds : bond 0.06198 ( 770) hydrogen bonds : angle 5.05853 ( 2169) metal coordination : bond 0.01068 ( 4) metal coordination : angle 12.32094 ( 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 296 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8771 (t0) cc_final: 0.8524 (t0) REVERT: A 120 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: A 121 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6256 (mt) REVERT: A 146 ARG cc_start: 0.8202 (mmt180) cc_final: 0.7981 (mmt180) REVERT: A 232 TYR cc_start: 0.8480 (t80) cc_final: 0.8266 (t80) REVERT: A 256 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7390 (tt0) REVERT: A 280 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: A 351 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7679 (mmtt) REVERT: A 412 ARG cc_start: 0.6211 (ttm110) cc_final: 0.5642 (mtt-85) REVERT: A 526 LYS cc_start: 0.8631 (mttm) cc_final: 0.8326 (mptt) REVERT: B 518 GLN cc_start: 0.7582 (mp10) cc_final: 0.7296 (mt0) REVERT: B 553 TYR cc_start: 0.6476 (t80) cc_final: 0.6261 (t80) REVERT: B 555 ASN cc_start: 0.7016 (m110) cc_final: 0.6686 (m110) REVERT: C 236 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6822 (p0) REVERT: C 280 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7855 (pp20) REVERT: C 291 TRP cc_start: 0.7194 (t-100) cc_final: 0.6570 (t60) REVERT: C 336 ARG cc_start: 0.7912 (mmp80) cc_final: 0.7375 (ttm-80) REVERT: C 373 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7279 (pp) REVERT: C 389 GLN cc_start: 0.7317 (mp10) cc_final: 0.6857 (mp10) REVERT: C 479 MET cc_start: 0.8892 (mmt) cc_final: 0.8473 (mmm) REVERT: C 517 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6849 (tp30) REVERT: D 301 HIS cc_start: 0.7563 (p-80) cc_final: 0.7193 (p90) REVERT: D 344 ARG cc_start: 0.6645 (mtp180) cc_final: 0.5007 (mpt90) REVERT: D 430 LEU cc_start: 0.5794 (mt) cc_final: 0.5322 (mp) REVERT: D 516 MET cc_start: 0.5071 (mmm) cc_final: 0.4827 (mmm) REVERT: E 2 GLU cc_start: 0.8072 (tt0) cc_final: 0.7820 (tt0) REVERT: E 9 TYR cc_start: 0.8528 (p90) cc_final: 0.8246 (p90) REVERT: E 61 ASP cc_start: 0.8573 (m-30) cc_final: 0.8247 (m-30) REVERT: E 65 ILE cc_start: 0.8943 (pt) cc_final: 0.8660 (mt) REVERT: E 88 ILE cc_start: 0.8889 (mm) cc_final: 0.8612 (mt) REVERT: F 91 GLN cc_start: 0.8381 (pm20) cc_final: 0.7963 (pm20) outliers start: 53 outliers final: 28 residues processed: 283 average time/residue: 0.1334 time to fit residues: 53.9436 Evaluate side-chains 229 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 121 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 280 GLU Chi-restraints excluded: chain A residue 441 VAL 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 303 ASN 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 B residue 536 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 337 THR 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 524 ILE Chi-restraints excluded: chain E residue 55 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 106 optimal weight: 30.0000 chunk 150 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS 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 = 0.4010 r_free = 0.4010 target = 0.148718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102194 restraints weight = 28489.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105552 restraints weight = 14461.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.107722 restraints weight = 9629.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109281 restraints weight = 7549.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110225 restraints weight = 6424.876| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15945 Z= 0.213 Angle : 0.764 19.343 21847 Z= 0.387 Chirality : 0.046 0.149 2361 Planarity : 0.006 0.112 2644 Dihedral : 17.238 139.250 2696 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.30 % Allowed : 17.99 % Favored : 77.72 % 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: -0.70 (0.19), residues: 1773 helix: 0.93 (0.18), residues: 848 sheet: -0.54 (0.42), residues: 134 loop : -2.07 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 412 TYR 0.017 0.002 TYR B 527 PHE 0.017 0.002 PHE B 407 TRP 0.022 0.002 TRP F 30 HIS 0.007 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00498 (15941) covalent geometry : angle 0.73588 (21835) hydrogen bonds : bond 0.06348 ( 770) hydrogen bonds : angle 4.83935 ( 2169) metal coordination : bond 0.00930 ( 4) metal coordination : angle 8.78032 ( 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 282 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 0.459 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: 0.9238 (mp) cc_final: 0.8978 (mp) REVERT: A 105 LYS cc_start: 0.8249 (mttm) cc_final: 0.7830 (mtmm) REVERT: A 120 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: A 479 MET cc_start: 0.7417 (ttm) cc_final: 0.7125 (ttm) REVERT: A 516 MET cc_start: 0.9022 (mmm) cc_final: 0.8320 (mmm) REVERT: A 536 GLU cc_start: 0.7922 (tt0) cc_final: 0.7405 (mt-10) REVERT: B 351 LYS cc_start: 0.7557 (tptt) cc_final: 0.7249 (tptt) REVERT: B 389 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7822 (mm-40) REVERT: C 236 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6605 (p0) REVERT: C 280 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8009 (pp20) REVERT: C 291 TRP cc_start: 0.7279 (t-100) cc_final: 0.6616 (t60) REVERT: C 293 MET cc_start: 0.5126 (mpp) cc_final: 0.4747 (mpp) REVERT: C 336 ARG cc_start: 0.7534 (mmp80) cc_final: 0.6745 (ttm-80) REVERT: C 373 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7265 (pp) REVERT: C 500 LEU cc_start: 0.7154 (mm) cc_final: 0.6892 (mm) REVERT: C 517 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7155 (tm-30) REVERT: C 536 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: D 344 ARG cc_start: 0.6842 (mtp180) cc_final: 0.5171 (mpt90) REVERT: D 358 MET cc_start: 0.6467 (mpt) cc_final: 0.5793 (ttp) REVERT: D 362 ASP cc_start: 0.7672 (m-30) cc_final: 0.7414 (t70) REVERT: D 403 MET cc_start: -0.1951 (mtp) cc_final: -0.2156 (mtm) REVERT: D 429 MET cc_start: 0.5476 (mmm) cc_final: 0.4285 (ptp) REVERT: D 431 THR cc_start: 0.6139 (p) cc_final: 0.5667 (p) REVERT: D 444 ASP cc_start: 0.7247 (t0) cc_final: 0.6942 (t0) REVERT: E 61 ASP cc_start: 0.8563 (m-30) cc_final: 0.8178 (m-30) REVERT: F 1 MET cc_start: 0.7495 (tpp) cc_final: 0.7262 (tpp) REVERT: F 91 GLN cc_start: 0.8540 (pm20) cc_final: 0.8128 (pm20) outliers start: 64 outliers final: 38 residues processed: 261 average time/residue: 0.1305 time to fit residues: 49.5961 Evaluate side-chains 230 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 181 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 476 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 530 SER 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 389 GLN Chi-restraints excluded: chain B residue 416 LYS 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 B residue 529 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP 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 C residue 436 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 536 GLU 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 360 LEU Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 8 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 138 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 90 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN C 312 GLN C 334 ASN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.149503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106360 restraints weight = 28343.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107508 restraints weight = 15127.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109409 restraints weight = 9730.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109798 restraints weight = 7841.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109914 restraints weight = 7298.148| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15945 Z= 0.146 Angle : 0.698 14.114 21847 Z= 0.351 Chirality : 0.043 0.228 2361 Planarity : 0.005 0.110 2644 Dihedral : 16.952 139.373 2691 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.15 % Allowed : 19.40 % Favored : 77.45 % 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: -0.42 (0.20), residues: 1773 helix: 1.16 (0.18), residues: 851 sheet: -0.54 (0.41), residues: 145 loop : -1.94 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 336 TYR 0.018 0.001 TYR B 387 PHE 0.016 0.001 PHE D 391 TRP 0.018 0.002 TRP F 30 HIS 0.006 0.001 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00329 (15941) covalent geometry : angle 0.67579 (21835) hydrogen bonds : bond 0.05839 ( 770) hydrogen bonds : angle 4.61948 ( 2169) metal coordination : bond 0.00463 ( 4) metal coordination : angle 7.45084 ( 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 248 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.539 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: 0.9249 (mp) cc_final: 0.9011 (mp) REVERT: A 43 ASP cc_start: 0.8835 (t0) cc_final: 0.8564 (t0) REVERT: A 105 LYS cc_start: 0.8177 (mttm) cc_final: 0.7801 (mtmm) REVERT: A 120 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: A 358 MET cc_start: 0.7480 (mmp) cc_final: 0.6114 (tmm) REVERT: A 479 MET cc_start: 0.7438 (ttm) cc_final: 0.6987 (ttm) REVERT: A 526 LYS cc_start: 0.8695 (mttm) cc_final: 0.8316 (mptt) REVERT: A 536 GLU cc_start: 0.7759 (tt0) cc_final: 0.7211 (mt-10) REVERT: B 389 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7854 (mm-40) REVERT: B 394 MET cc_start: 0.7641 (mtt) cc_final: 0.7353 (mtt) REVERT: B 416 LYS cc_start: 0.8037 (mmtp) cc_final: 0.7569 (tttt) REVERT: C 227 GLN cc_start: 0.8693 (pp30) cc_final: 0.7952 (pt0) REVERT: C 236 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6922 (p0) REVERT: C 291 TRP cc_start: 0.7399 (t-100) cc_final: 0.6693 (t60) REVERT: C 293 MET cc_start: 0.5263 (mpp) cc_final: 0.5037 (mpp) REVERT: C 500 LEU cc_start: 0.7320 (mm) cc_final: 0.7052 (mm) REVERT: C 517 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7093 (tp30) REVERT: D 301 HIS cc_start: 0.7772 (p-80) cc_final: 0.7448 (p90) REVERT: D 344 ARG cc_start: 0.6629 (mtp180) cc_final: 0.4923 (mpt90) REVERT: D 358 MET cc_start: 0.6469 (mpt) cc_final: 0.5641 (ttp) REVERT: D 429 MET cc_start: 0.6078 (mmm) cc_final: 0.4780 (ptp) REVERT: D 444 ASP cc_start: 0.7267 (t0) cc_final: 0.6984 (t0) REVERT: E 2 GLU cc_start: 0.7947 (tt0) cc_final: 0.7402 (tt0) REVERT: E 55 ILE cc_start: 0.8858 (mm) cc_final: 0.8546 (tt) REVERT: E 61 ASP cc_start: 0.8444 (m-30) cc_final: 0.8046 (m-30) REVERT: F 91 GLN cc_start: 0.8533 (pm20) cc_final: 0.8005 (pm20) outliers start: 47 outliers final: 30 residues processed: 231 average time/residue: 0.1380 time to fit residues: 46.1264 Evaluate side-chains 212 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN 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 441 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 281 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 B residue 529 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 478 LEU 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 360 LEU Chi-restraints excluded: chain D residue 412 ARG 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 13 ASN 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: 6.9990 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN D 366 HIS ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.148855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104724 restraints weight = 28821.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.104992 restraints weight = 16742.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106073 restraints weight = 11415.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106613 restraints weight = 9855.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106815 restraints weight = 8674.978| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15945 Z= 0.161 Angle : 0.700 13.464 21847 Z= 0.351 Chirality : 0.044 0.225 2361 Planarity : 0.005 0.107 2644 Dihedral : 16.714 139.367 2686 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.83 % Allowed : 20.27 % Favored : 75.91 % 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: 1.21 (0.18), residues: 851 sheet: -0.58 (0.40), residues: 155 loop : -1.86 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 336 TYR 0.015 0.001 TYR D 527 PHE 0.017 0.001 PHE D 391 TRP 0.019 0.001 TRP F 30 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00369 (15941) covalent geometry : angle 0.68021 (21835) hydrogen bonds : bond 0.05820 ( 770) hydrogen bonds : angle 4.57325 ( 2169) metal coordination : bond 0.00558 ( 4) metal coordination : angle 7.03899 ( 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 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 0.538 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: 0.9263 (mp) cc_final: 0.9045 (mp) REVERT: A 43 ASP cc_start: 0.8849 (t0) cc_final: 0.8573 (t0) REVERT: A 105 LYS cc_start: 0.8260 (mttm) cc_final: 0.7841 (mtmm) REVERT: A 120 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 227 GLN cc_start: 0.8386 (pp30) cc_final: 0.8178 (pp30) REVERT: A 358 MET cc_start: 0.7614 (mmp) cc_final: 0.6190 (tmm) REVERT: A 479 MET cc_start: 0.7538 (ttm) cc_final: 0.7128 (ttm) REVERT: A 526 LYS cc_start: 0.8736 (mttm) cc_final: 0.8322 (pttm) REVERT: A 536 GLU cc_start: 0.7841 (tt0) cc_final: 0.7317 (mt-10) REVERT: C 227 GLN cc_start: 0.8712 (pp30) cc_final: 0.8010 (pt0) REVERT: C 236 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7090 (p0) REVERT: C 291 TRP cc_start: 0.7443 (t-100) cc_final: 0.6795 (t60) REVERT: C 336 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7196 (mmm160) REVERT: C 500 LEU cc_start: 0.7215 (mm) cc_final: 0.6959 (mm) REVERT: C 517 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7119 (tp30) REVERT: C 536 GLU cc_start: 0.8088 (pm20) cc_final: 0.7757 (pm20) REVERT: D 230 LYS cc_start: 0.5287 (OUTLIER) cc_final: 0.3997 (tppt) REVERT: D 301 HIS cc_start: 0.7801 (p-80) cc_final: 0.7472 (p90) REVERT: D 344 ARG cc_start: 0.6588 (mtp180) cc_final: 0.4895 (mpt90) REVERT: D 358 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5624 (ttp) REVERT: D 429 MET cc_start: 0.6330 (mmm) cc_final: 0.5046 (ptp) REVERT: D 451 HIS cc_start: 0.3678 (OUTLIER) cc_final: 0.2678 (m-70) REVERT: E 61 ASP cc_start: 0.8443 (m-30) cc_final: 0.8057 (m-30) REVERT: F 2 GLU cc_start: 0.8115 (tt0) cc_final: 0.7820 (tt0) REVERT: F 91 GLN cc_start: 0.8517 (pm20) cc_final: 0.7980 (pm20) outliers start: 57 outliers final: 35 residues processed: 249 average time/residue: 0.1441 time to fit residues: 50.7992 Evaluate side-chains 230 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN 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 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 377 LEU 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 298 SER Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 412 ARG 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 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: 0.9990 chunk 162 optimal weight: 2.9990 chunk 58 optimal weight: 0.0070 chunk 109 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 17 optimal weight: 0.0170 chunk 52 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN B 411 ASN C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** 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 = 0.4045 r_free = 0.4045 target = 0.150841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108122 restraints weight = 27954.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110197 restraints weight = 15057.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111339 restraints weight = 9665.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111515 restraints weight = 7603.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.111901 restraints weight = 7167.475| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15945 Z= 0.130 Angle : 0.676 14.054 21847 Z= 0.338 Chirality : 0.042 0.198 2361 Planarity : 0.005 0.101 2644 Dihedral : 16.627 139.426 2686 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.22 % Allowed : 21.21 % Favored : 75.57 % 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: -0.21 (0.20), residues: 1773 helix: 1.33 (0.18), residues: 844 sheet: -0.80 (0.38), residues: 176 loop : -1.73 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 19 TYR 0.015 0.001 TYR D 527 PHE 0.019 0.001 PHE D 391 TRP 0.015 0.001 TRP F 30 HIS 0.004 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00290 (15941) covalent geometry : angle 0.66135 (21835) hydrogen bonds : bond 0.05441 ( 770) hydrogen bonds : angle 4.41084 ( 2169) metal coordination : bond 0.00374 ( 4) metal coordination : angle 6.06746 ( 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 265 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 0.560 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: 0.9241 (mp) cc_final: 0.9039 (mp) REVERT: A 43 ASP cc_start: 0.8747 (t0) cc_final: 0.8500 (t0) REVERT: A 105 LYS cc_start: 0.8147 (mttm) cc_final: 0.7834 (mtmm) REVERT: A 120 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: A 358 MET cc_start: 0.7241 (mmp) cc_final: 0.6023 (tmm) REVERT: A 479 MET cc_start: 0.7570 (ttm) cc_final: 0.7194 (ttm) REVERT: A 516 MET cc_start: 0.8768 (mmm) cc_final: 0.8257 (mtp) REVERT: A 526 LYS cc_start: 0.8758 (mttm) cc_final: 0.8322 (pttm) REVERT: A 536 GLU cc_start: 0.7730 (tt0) cc_final: 0.7307 (mt-10) REVERT: B 351 LYS cc_start: 0.7478 (tptt) cc_final: 0.6848 (tptt) REVERT: C 227 GLN cc_start: 0.8680 (pp30) cc_final: 0.7990 (pt0) REVERT: C 291 TRP cc_start: 0.7350 (t-100) cc_final: 0.6617 (t60) REVERT: C 336 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6970 (mmm160) REVERT: C 434 TRP cc_start: 0.8004 (m100) cc_final: 0.7781 (m100) REVERT: C 517 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7089 (tp30) REVERT: C 519 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 230 LYS cc_start: 0.5156 (OUTLIER) cc_final: 0.3871 (tppt) REVERT: D 301 HIS cc_start: 0.7817 (p-80) cc_final: 0.6854 (p90) REVERT: D 358 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5654 (ttp) REVERT: D 360 LEU cc_start: 0.6169 (tp) cc_final: 0.5841 (tp) REVERT: D 429 MET cc_start: 0.6267 (mmm) cc_final: 0.5066 (ptp) REVERT: D 451 HIS cc_start: 0.3467 (OUTLIER) cc_final: 0.2506 (m-70) REVERT: E 61 ASP cc_start: 0.8415 (m-30) cc_final: 0.8135 (m-30) REVERT: E 88 ILE cc_start: 0.8976 (mm) cc_final: 0.8748 (mt) REVERT: F 75 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7461 (mmmt) REVERT: F 91 GLN cc_start: 0.8504 (pm20) cc_final: 0.7929 (pm20) outliers start: 48 outliers final: 25 residues processed: 249 average time/residue: 0.1367 time to fit residues: 49.5387 Evaluate side-chains 222 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 336 ARG 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 D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 13 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 21 optimal weight: 0.0050 chunk 64 optimal weight: 0.8980 chunk 144 optimal weight: 0.0980 chunk 26 optimal weight: 0.4980 chunk 121 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 GLN D 312 GLN D 451 HIS ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.151008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108295 restraints weight = 28919.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108606 restraints weight = 16099.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109877 restraints weight = 11261.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110149 restraints weight = 9802.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110353 restraints weight = 8486.162| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15945 Z= 0.133 Angle : 0.670 13.763 21847 Z= 0.338 Chirality : 0.042 0.184 2361 Planarity : 0.006 0.127 2644 Dihedral : 16.595 139.597 2686 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.68 % Allowed : 22.55 % Favored : 74.77 % 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: -0.19 (0.20), residues: 1773 helix: 1.34 (0.18), residues: 843 sheet: -0.80 (0.38), residues: 179 loop : -1.70 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 336 TYR 0.015 0.001 TYR D 527 PHE 0.015 0.001 PHE D 391 TRP 0.021 0.001 TRP B 343 HIS 0.007 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00300 (15941) covalent geometry : angle 0.65493 (21835) hydrogen bonds : bond 0.05403 ( 770) hydrogen bonds : angle 4.39931 ( 2169) metal coordination : bond 0.00418 ( 4) metal coordination : angle 6.01214 ( 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 245 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.446 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: 0.9239 (mp) cc_final: 0.8984 (mp) REVERT: A 43 ASP cc_start: 0.8720 (t0) cc_final: 0.8486 (t0) REVERT: A 105 LYS cc_start: 0.8141 (mttm) cc_final: 0.7776 (mtmm) REVERT: A 120 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: A 358 MET cc_start: 0.7254 (mmp) cc_final: 0.6045 (tmm) REVERT: A 462 LEU cc_start: 0.8577 (tp) cc_final: 0.7902 (tp) REVERT: A 479 MET cc_start: 0.7583 (ttm) cc_final: 0.7219 (ttm) REVERT: A 516 MET cc_start: 0.8802 (mmm) cc_final: 0.8117 (mtp) REVERT: A 526 LYS cc_start: 0.8752 (mttm) cc_final: 0.8328 (pttm) REVERT: A 536 GLU cc_start: 0.7728 (tt0) cc_final: 0.7321 (mt-10) REVERT: C 227 GLN cc_start: 0.8680 (pp30) cc_final: 0.8016 (pt0) REVERT: C 291 TRP cc_start: 0.7287 (t-100) cc_final: 0.6648 (t60) REVERT: C 293 MET cc_start: 0.5166 (mpp) cc_final: 0.4921 (mpp) REVERT: C 336 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7061 (mmm160) REVERT: C 434 TRP cc_start: 0.8034 (m100) cc_final: 0.7755 (m100) REVERT: C 517 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7309 (tp30) REVERT: D 230 LYS cc_start: 0.5113 (OUTLIER) cc_final: 0.3772 (tppt) REVERT: D 253 ARG cc_start: 0.7333 (tpt90) cc_final: 0.6353 (ptm-80) REVERT: D 259 GLN cc_start: 0.5199 (pm20) cc_final: 0.4939 (pm20) REVERT: D 301 HIS cc_start: 0.7661 (p-80) cc_final: 0.7317 (p90) REVERT: D 358 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5566 (ttp) REVERT: D 429 MET cc_start: 0.6347 (mmm) cc_final: 0.5086 (ptp) REVERT: D 451 HIS cc_start: 0.3453 (OUTLIER) cc_final: 0.2277 (m90) REVERT: E 25 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.7884 (m-70) REVERT: E 61 ASP cc_start: 0.8397 (m-30) cc_final: 0.8127 (m-30) REVERT: E 88 ILE cc_start: 0.8815 (mm) cc_final: 0.8567 (mt) REVERT: F 75 LYS cc_start: 0.7758 (mmmt) cc_final: 0.7500 (mmmt) REVERT: F 91 GLN cc_start: 0.8471 (pm20) cc_final: 0.7896 (pm20) outliers start: 40 outliers final: 25 residues processed: 227 average time/residue: 0.1323 time to fit residues: 43.1961 Evaluate side-chains 218 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 435 THR 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 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 322 ASN Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 51 optimal weight: 0.0670 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN D 451 HIS ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.150991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103740 restraints weight = 28704.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107405 restraints weight = 14505.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.109680 restraints weight = 9580.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111188 restraints weight = 7477.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111962 restraints weight = 6441.764| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.7210 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= 0.140 Angle : 0.689 13.586 21847 Z= 0.348 Chirality : 0.042 0.168 2361 Planarity : 0.005 0.093 2644 Dihedral : 16.579 139.144 2686 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.55 % Allowed : 23.09 % Favored : 74.36 % 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: -0.19 (0.20), residues: 1773 helix: 1.32 (0.18), residues: 843 sheet: -0.69 (0.39), residues: 175 loop : -1.70 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 336 TYR 0.021 0.001 TYR D 450 PHE 0.015 0.001 PHE D 391 TRP 0.022 0.001 TRP D 327 HIS 0.021 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00318 (15941) covalent geometry : angle 0.67424 (21835) hydrogen bonds : bond 0.05460 ( 770) hydrogen bonds : angle 4.46433 ( 2169) metal coordination : bond 0.00435 ( 4) metal coordination : angle 6.00118 ( 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 240 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.579 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: 0.9236 (mp) cc_final: 0.8988 (mp) REVERT: A 43 ASP cc_start: 0.8749 (t0) cc_final: 0.8497 (t0) REVERT: A 105 LYS cc_start: 0.8105 (mttm) cc_final: 0.7787 (mtmm) REVERT: A 120 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: A 358 MET cc_start: 0.7155 (mmp) cc_final: 0.6105 (tmm) REVERT: A 462 LEU cc_start: 0.8583 (tp) cc_final: 0.8296 (mp) REVERT: A 479 MET cc_start: 0.7576 (ttm) cc_final: 0.7220 (ttm) REVERT: A 516 MET cc_start: 0.8829 (mmm) cc_final: 0.8079 (mtp) REVERT: A 526 LYS cc_start: 0.8741 (mttm) cc_final: 0.8296 (pttm) REVERT: A 536 GLU cc_start: 0.7867 (tt0) cc_final: 0.7425 (mt-10) REVERT: C 227 GLN cc_start: 0.8683 (pp30) cc_final: 0.8023 (pt0) REVERT: C 291 TRP cc_start: 0.7212 (t-100) cc_final: 0.6494 (t60) REVERT: C 293 MET cc_start: 0.4979 (mpp) cc_final: 0.4711 (mpp) REVERT: C 336 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7046 (mmm160) REVERT: C 358 MET cc_start: 0.8568 (ppp) cc_final: 0.8099 (ppp) REVERT: D 230 LYS cc_start: 0.5124 (OUTLIER) cc_final: 0.3730 (tppt) REVERT: D 253 ARG cc_start: 0.7375 (tpt90) cc_final: 0.6373 (ptm-80) REVERT: D 259 GLN cc_start: 0.5088 (pm20) cc_final: 0.4881 (pm20) REVERT: D 301 HIS cc_start: 0.7744 (p-80) cc_final: 0.7412 (p90) REVERT: D 358 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5621 (ttp) REVERT: D 429 MET cc_start: 0.5881 (mmm) cc_final: 0.5044 (mtm) REVERT: E 25 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.7875 (m-70) REVERT: E 61 ASP cc_start: 0.8410 (m-30) cc_final: 0.8156 (m-30) REVERT: E 88 ILE cc_start: 0.8778 (mm) cc_final: 0.8519 (mt) REVERT: F 91 GLN cc_start: 0.8423 (pm20) cc_final: 0.7782 (pm20) outliers start: 38 outliers final: 26 residues processed: 226 average time/residue: 0.1325 time to fit residues: 43.4107 Evaluate side-chains 215 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 192 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 520 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 435 THR 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 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 322 ASN Chi-restraints excluded: chain C residue 336 ARG 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 D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 93 VAL 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 124 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.149600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106446 restraints weight = 27977.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109330 restraints weight = 14289.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110206 restraints weight = 8611.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.110531 restraints weight = 7438.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110818 restraints weight = 6948.323| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15945 Z= 0.142 Angle : 0.701 13.467 21847 Z= 0.352 Chirality : 0.044 0.467 2361 Planarity : 0.005 0.093 2644 Dihedral : 16.570 138.906 2686 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.35 % Allowed : 23.36 % Favored : 74.30 % 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: -0.13 (0.20), residues: 1773 helix: 1.37 (0.18), residues: 843 sheet: -0.48 (0.40), residues: 159 loop : -1.71 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 336 TYR 0.020 0.001 TYR B 387 PHE 0.015 0.001 PHE D 391 TRP 0.022 0.001 TRP D 327 HIS 0.005 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00327 (15941) covalent geometry : angle 0.68709 (21835) hydrogen bonds : bond 0.05471 ( 770) hydrogen bonds : angle 4.44481 ( 2169) metal coordination : bond 0.00453 ( 4) metal coordination : angle 5.99377 ( 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 230 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.410 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: 0.9244 (mp) cc_final: 0.8995 (mp) REVERT: A 43 ASP cc_start: 0.8778 (t0) cc_final: 0.8524 (t0) REVERT: A 105 LYS cc_start: 0.8111 (mttm) cc_final: 0.7825 (mtmm) REVERT: A 120 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: A 358 MET cc_start: 0.7232 (mmp) cc_final: 0.6190 (tmm) REVERT: A 462 LEU cc_start: 0.8591 (tp) cc_final: 0.7992 (tp) REVERT: A 479 MET cc_start: 0.7562 (ttm) cc_final: 0.7195 (ttm) REVERT: A 516 MET cc_start: 0.8826 (mmm) cc_final: 0.8071 (mtp) REVERT: A 526 LYS cc_start: 0.8753 (mttm) cc_final: 0.8299 (pttm) REVERT: A 536 GLU cc_start: 0.7857 (tt0) cc_final: 0.7447 (mt-10) REVERT: B 366 HIS cc_start: 0.7833 (m-70) cc_final: 0.7446 (m-70) REVERT: C 227 GLN cc_start: 0.8676 (pp30) cc_final: 0.8001 (pt0) REVERT: C 291 TRP cc_start: 0.7326 (t-100) cc_final: 0.6633 (t60) REVERT: C 293 MET cc_start: 0.5213 (mpp) cc_final: 0.4971 (mpp) REVERT: C 336 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7090 (mmm160) REVERT: C 358 MET cc_start: 0.8614 (ppp) cc_final: 0.8047 (ppp) REVERT: C 500 LEU cc_start: 0.7297 (mm) cc_final: 0.7054 (mm) REVERT: D 230 LYS cc_start: 0.5119 (OUTLIER) cc_final: 0.3651 (tppt) REVERT: D 253 ARG cc_start: 0.7373 (tpt90) cc_final: 0.6387 (ptm-80) REVERT: D 259 GLN cc_start: 0.5363 (pm20) cc_final: 0.5117 (pm20) REVERT: D 301 HIS cc_start: 0.7802 (p-80) cc_final: 0.7514 (p90) REVERT: D 358 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5201 (ttp) REVERT: D 429 MET cc_start: 0.6493 (mmm) cc_final: 0.5430 (ptp) REVERT: D 430 LEU cc_start: 0.6812 (mm) cc_final: 0.6576 (mm) REVERT: E 25 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.7840 (m-70) REVERT: E 61 ASP cc_start: 0.8412 (m-30) cc_final: 0.8081 (m-30) REVERT: E 88 ILE cc_start: 0.8800 (mm) cc_final: 0.8550 (mt) REVERT: F 75 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7643 (mmmt) REVERT: F 91 GLN cc_start: 0.8419 (pm20) cc_final: 0.7822 (pm20) outliers start: 35 outliers final: 27 residues processed: 217 average time/residue: 0.1290 time to fit residues: 40.9383 Evaluate side-chains 220 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 192 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 520 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 435 THR 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 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 322 ASN Chi-restraints excluded: chain C residue 336 ARG 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 D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 13 ASN 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: 0.3980 chunk 145 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.149407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105708 restraints weight = 28639.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105976 restraints weight = 17078.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107504 restraints weight = 10973.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107773 restraints weight = 9291.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108013 restraints weight = 8427.442| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.7436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15945 Z= 0.148 Angle : 0.701 13.395 21847 Z= 0.353 Chirality : 0.043 0.370 2361 Planarity : 0.005 0.092 2644 Dihedral : 16.586 138.840 2686 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.55 % Allowed : 23.49 % Favored : 73.96 % 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: -0.13 (0.20), residues: 1773 helix: 1.38 (0.18), residues: 843 sheet: -0.51 (0.40), residues: 159 loop : -1.71 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 12 TYR 0.014 0.001 TYR D 527 PHE 0.015 0.001 PHE D 391 TRP 0.020 0.001 TRP D 327 HIS 0.012 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00345 (15941) covalent geometry : angle 0.68669 (21835) hydrogen bonds : bond 0.05541 ( 770) hydrogen bonds : angle 4.45017 ( 2169) metal coordination : bond 0.00490 ( 4) metal coordination : angle 6.07668 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.98 seconds wall clock time: 49 minutes 22.36 seconds (2962.36 seconds total)