Starting phenix.real_space_refine on Fri Jul 3 18:25:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi5_23840/07_2026/7mi5_23840_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi5_23840/07_2026/7mi5_23840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mi5_23840/07_2026/7mi5_23840_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi5_23840/07_2026/7mi5_23840_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mi5_23840/07_2026/7mi5_23840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi5_23840/07_2026/7mi5_23840.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 6 7.51 5 Fe 4 7.16 5 P 60 5.49 5 S 87 5.16 5 C 9573 2.51 5 N 2847 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15469 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4347 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 35, 'TRANS': 517} Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2711 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "C" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2887 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 22, 'TRANS': 339} Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "H" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 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: 4.34, per 1000 atoms: 0.28 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: 1.48 Conformation dependent library (CDL) restraints added in 677.3 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: 1.75 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: 3.12 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 6894 1.42 - 1.63: 8898 1.63 - 1.85: 137 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 15941 Sorted by residual: bond pdb=" C1' DG H 20 " pdb=" N9 DG H 20 " ideal model delta sigma weight residual 1.468 1.360 0.108 1.40e-02 5.10e+03 5.94e+01 bond pdb=" C1' DA H 21 " pdb=" N9 DA H 21 " ideal model delta sigma weight residual 1.468 1.368 0.100 1.40e-02 5.10e+03 5.06e+01 bond pdb=" C1' DC H 19 " pdb=" N1 DC H 19 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" N1 DC G 15 " pdb=" C6 DC G 15 " ideal model delta sigma weight residual 1.367 1.343 0.024 6.00e-03 2.78e+04 1.64e+01 bond pdb=" C3' DC H 15 " pdb=" C2' DC H 15 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.56e+01 ... (remaining 15936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.40: 21697 6.40 - 12.80: 112 12.80 - 19.20: 17 19.20 - 25.60: 5 25.60 - 32.00: 4 Bond angle restraints: 21835 Sorted by residual: angle pdb=" CA MET D 364 " pdb=" CB MET D 364 " pdb=" CG MET D 364 " ideal model delta sigma weight residual 114.10 139.65 -25.55 2.00e+00 2.50e-01 1.63e+02 angle pdb=" CA MET B 364 " pdb=" CB MET B 364 " pdb=" CG MET B 364 " ideal model delta sigma weight residual 114.10 139.62 -25.52 2.00e+00 2.50e-01 1.63e+02 angle pdb=" CA MET D 479 " pdb=" CB MET D 479 " pdb=" CG MET D 479 " ideal model delta sigma weight residual 114.10 137.14 -23.04 2.00e+00 2.50e-01 1.33e+02 angle pdb=" CA MET B 479 " pdb=" CB MET B 479 " pdb=" CG MET B 479 " ideal model delta sigma weight residual 114.10 137.14 -23.04 2.00e+00 2.50e-01 1.33e+02 angle pdb=" CB MET B 479 " pdb=" CG MET B 479 " pdb=" SD MET B 479 " ideal model delta sigma weight residual 112.70 144.70 -32.00 3.00e+00 1.11e-01 1.14e+02 ... (remaining 21830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.22: 8506 29.22 - 58.43: 797 58.43 - 87.65: 103 87.65 - 116.87: 4 116.87 - 146.08: 2 Dihedral angle restraints: 9412 sinusoidal: 4289 harmonic: 5123 Sorted by residual: dihedral pdb=" CA ARG B 412 " pdb=" C ARG B 412 " pdb=" N ARG B 413 " pdb=" CA ARG B 413 " ideal model delta harmonic sigma weight residual -180.00 -145.33 -34.67 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA ARG D 412 " pdb=" C ARG D 412 " pdb=" N ARG D 413 " pdb=" CA ARG D 413 " ideal model delta harmonic sigma weight residual -180.00 -145.36 -34.64 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CA GLN C 312 " pdb=" C GLN C 312 " pdb=" N ARG C 313 " pdb=" CA ARG C 313 " ideal model delta harmonic sigma weight residual 180.00 149.32 30.68 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 9409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1974 0.084 - 0.169: 331 0.169 - 0.253: 47 0.253 - 0.338: 7 0.338 - 0.422: 2 Chirality restraints: 2361 Sorted by residual: chirality pdb=" CA MET B 364 " pdb=" N MET B 364 " pdb=" C MET B 364 " pdb=" CB MET B 364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA MET D 364 " pdb=" N MET D 364 " pdb=" C MET D 364 " pdb=" CB MET D 364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA TYR A 232 " pdb=" N TYR A 232 " pdb=" C TYR A 232 " pdb=" CB TYR A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2358 not shown) Planarity restraints: 2644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 327 " 0.029 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP D 327 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP D 327 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP D 327 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 327 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 327 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 327 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 327 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 327 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 327 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 327 " -0.029 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP B 327 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP B 327 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP B 327 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 327 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 327 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 327 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 327 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 327 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 327 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 340 " 0.061 9.50e-02 1.11e+02 3.44e-02 5.96e+00 pdb=" NE ARG B 340 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 340 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG B 340 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 340 " -0.012 2.00e-02 2.50e+03 ... (remaining 2641 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 124 2.31 - 2.96: 8814 2.96 - 3.60: 25515 3.60 - 4.25: 38226 4.25 - 4.90: 60951 Nonbonded interactions: 133630 Sorted by model distance: nonbonded pdb=" N2 DG G 8 " pdb=" N3 DG H 20 " model vdw 1.662 3.200 nonbonded pdb=" OP1 DG H 32 " pdb="MN MN H 801 " model vdw 1.716 3.060 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 3.140 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: 1.010 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.720 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.362 15945 Z= 0.554 Angle : 1.615 60.520 21847 Z= 0.825 Chirality : 0.065 0.422 2361 Planarity : 0.006 0.045 2644 Dihedral : 21.219 146.085 6130 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 35.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.42 % Favored : 90.47 % Rotamer: Outliers : 11.95 % Allowed : 2.28 % Favored : 85.77 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.18), residues: 1773 helix: -1.06 (0.16), residues: 822 sheet: -0.81 (0.46), residues: 124 loop : -2.33 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.003 ARG B 340 TYR 0.026 0.003 TYR C 311 PHE 0.021 0.003 PHE D 491 TRP 0.078 0.004 TRP D 327 HIS 0.017 0.002 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00977 / 0.55 (15941) covalent geometry : angle 1.47886 / 0.82 (21835) hydrogen bonds : bond 0.17744 / 12.16 ( 770) hydrogen bonds : angle 8.00788 / 5.71 ( 2169) metal coordination : bond 0.18912 / 11.76 ( 4) metal coordination : angle 27.70161 / 14.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 483 time to evaluate : 0.561 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: 0.1843 time to fit residues: 141.3921 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 : 0.453 ------------------------------------------------------------------------------- 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... A 32 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN B 522 HIS C 310 GLN C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 451 HIS ** D 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.162115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116042 restraints weight = 28930.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120154 restraints weight = 14489.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123048 restraints weight = 9416.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124798 restraints weight = 7152.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125982 restraints weight = 6021.593| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15945 Z= 0.214 Angle : 1.061 55.003 21847 Z= 0.475 Chirality : 0.052 0.222 2361 Planarity : 0.007 0.121 2644 Dihedral : 18.603 138.122 2797 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.28 % Favored : 92.67 % Rotamer: Outliers : 5.10 % Allowed : 14.09 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.18), residues: 1773 helix: -0.24 (0.17), residues: 837 sheet: -0.73 (0.46), residues: 120 loop : -2.21 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG D 369 TYR 0.027 0.002 TYR A 553 PHE 0.026 0.002 PHE A 153 TRP 0.038 0.003 TRP D 327 HIS 0.011 0.002 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (15941) covalent geometry : angle 0.89274 / 0.47 (21835) hydrogen bonds : bond 0.07545 / 4.80 ( 770) hydrogen bonds : angle 5.88498 / 4.23 ( 2169) metal coordination : bond 0.01812 / 1.10 ( 4) metal coordination : angle 24.46530 / 12.80 ( 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 364 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 288 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8192 (ttm) cc_final: 0.7670 (ttm) REVERT: A 43 ASP cc_start: 0.8779 (t0) cc_final: 0.8463 (t0) REVERT: A 256 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7214 (tt0) REVERT: A 358 MET cc_start: 0.6333 (mmm) cc_final: 0.6106 (ppp) REVERT: A 524 ILE cc_start: 0.7465 (mp) cc_final: 0.7227 (mp) REVERT: A 526 LYS cc_start: 0.8161 (mttm) cc_final: 0.7947 (mptt) REVERT: B 389 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: C 227 GLN cc_start: 0.8413 (pp30) cc_final: 0.7803 (pt0) REVERT: C 259 GLN cc_start: 0.8447 (mt0) cc_final: 0.8178 (mt0) REVERT: C 265 ASN cc_start: 0.8127 (m-40) cc_final: 0.7647 (t0) REVERT: C 280 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7408 (pp20) REVERT: C 291 TRP cc_start: 0.7166 (t-100) cc_final: 0.6189 (t60) REVERT: C 336 ARG cc_start: 0.7599 (mmp80) cc_final: 0.6701 (mmm160) REVERT: C 373 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7341 (mp) REVERT: C 418 PRO cc_start: 0.8467 (Cg_exo) cc_final: 0.8245 (Cg_endo) REVERT: C 479 MET cc_start: 0.8831 (mmt) cc_final: 0.8261 (mmm) REVERT: C 483 ASN cc_start: 0.8582 (m-40) cc_final: 0.8122 (m-40) REVERT: C 517 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6877 (tp30) REVERT: D 301 HIS cc_start: 0.7538 (p-80) cc_final: 0.6876 (p90) REVERT: D 302 ARG cc_start: 0.6296 (tpp-160) cc_final: 0.6022 (tpt90) REVERT: D 318 GLU cc_start: 0.5949 (pp20) cc_final: 0.5738 (mp0) REVERT: D 358 MET cc_start: 0.6695 (mpp) cc_final: 0.6432 (mpp) REVERT: D 379 ILE cc_start: 0.2136 (OUTLIER) cc_final: 0.1646 (tp) REVERT: D 394 MET cc_start: 0.5153 (mmt) cc_final: 0.4279 (mmt) REVERT: D 430 LEU cc_start: 0.5511 (mt) cc_final: 0.5005 (mp) REVERT: D 457 ARG cc_start: 0.7354 (mtm180) cc_final: 0.6959 (mtm-85) REVERT: E 47 LYS cc_start: 0.8951 (mttm) cc_final: 0.8490 (mttt) REVERT: E 54 GLU cc_start: 0.7357 (pp20) cc_final: 0.7065 (pp20) REVERT: E 61 ASP cc_start: 0.8347 (m-30) cc_final: 0.7991 (m-30) REVERT: E 75 LYS cc_start: 0.8395 (ptpp) cc_final: 0.8099 (tptp) REVERT: F 91 GLN cc_start: 0.8548 (pm20) cc_final: 0.8247 (pm20) outliers start: 76 outliers final: 33 residues processed: 335 average time/residue: 0.1436 time to fit residues: 69.0329 Evaluate side-chains 263 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 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 13 ASN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 71 optimal weight: 0.8980 chunk 179 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 78 optimal weight: 0.0010 chunk 148 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 420 ASN B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** D 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.160078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.116545 restraints weight = 29150.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118894 restraints weight = 15612.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120948 restraints weight = 10216.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.121293 restraints weight = 7357.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121897 restraints weight = 7360.372| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15945 Z= 0.169 Angle : 0.897 42.645 21847 Z= 0.412 Chirality : 0.047 0.213 2361 Planarity : 0.006 0.116 2644 Dihedral : 17.449 137.149 2705 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.94 % Favored : 93.01 % Rotamer: Outliers : 3.56 % Allowed : 17.92 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 1773 helix: 0.34 (0.17), residues: 832 sheet: -1.05 (0.42), residues: 135 loop : -2.08 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 515 TYR 0.027 0.002 TYR A 21 PHE 0.018 0.002 PHE A 153 TRP 0.016 0.002 TRP B 327 HIS 0.007 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (15941) covalent geometry : angle 0.78096 / 0.41 (21835) hydrogen bonds : bond 0.06635 / 4.30 ( 770) hydrogen bonds : angle 5.32575 / 3.83 ( 2169) metal coordination : bond 0.00985 / 0.59 ( 4) metal coordination : angle 18.83307 / 10.10 ( 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 300 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8749 (t0) cc_final: 0.8512 (t0) REVERT: A 105 LYS cc_start: 0.8208 (mttm) cc_final: 0.7992 (ttmm) REVERT: A 232 TYR cc_start: 0.8382 (t80) cc_final: 0.7776 (t80) REVERT: A 256 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7203 (tt0) REVERT: A 351 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7446 (mmtt) REVERT: A 526 LYS cc_start: 0.8462 (mttm) cc_final: 0.8162 (mptt) REVERT: B 395 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6940 (tp) REVERT: B 518 GLN cc_start: 0.7358 (mt0) cc_final: 0.7098 (mt0) REVERT: B 538 GLN cc_start: 0.7877 (mm110) cc_final: 0.7578 (mm-40) REVERT: B 555 ASN cc_start: 0.6991 (m110) cc_final: 0.6552 (m110) REVERT: C 227 GLN cc_start: 0.8481 (pp30) cc_final: 0.7820 (pt0) REVERT: C 259 GLN cc_start: 0.8514 (mt0) cc_final: 0.8297 (mt0) REVERT: C 265 ASN cc_start: 0.8194 (m-40) cc_final: 0.7647 (t0) REVERT: C 280 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7653 (pp20) REVERT: C 291 TRP cc_start: 0.6975 (t-100) cc_final: 0.6303 (t60) REVERT: C 336 ARG cc_start: 0.7677 (mmp80) cc_final: 0.7246 (mmm160) REVERT: C 373 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7332 (pp) REVERT: C 479 MET cc_start: 0.8921 (mmt) cc_final: 0.8436 (mmm) REVERT: C 483 ASN cc_start: 0.8691 (m-40) cc_final: 0.8315 (m-40) REVERT: C 517 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6770 (tp30) REVERT: C 535 LEU cc_start: 0.6707 (mt) cc_final: 0.6327 (mt) REVERT: D 301 HIS cc_start: 0.7397 (p-80) cc_final: 0.6948 (p90) REVERT: D 344 ARG cc_start: 0.6710 (mtp180) cc_final: 0.5049 (mpt180) REVERT: D 358 MET cc_start: 0.6591 (mpp) cc_final: 0.6385 (mpp) REVERT: D 379 ILE cc_start: 0.2944 (OUTLIER) cc_final: 0.2556 (tp) REVERT: D 394 MET cc_start: 0.4342 (mmt) cc_final: 0.3658 (mmt) REVERT: D 429 MET cc_start: 0.5997 (mmt) cc_final: 0.4712 (ptp) REVERT: D 430 LEU cc_start: 0.5596 (mt) cc_final: 0.5155 (mp) REVERT: D 479 MET cc_start: 0.3216 (mmt) cc_final: 0.1377 (tpt) REVERT: E 22 LYS cc_start: 0.8751 (pptt) cc_final: 0.8251 (pttm) REVERT: E 47 LYS cc_start: 0.9008 (mttm) cc_final: 0.8565 (mttt) REVERT: E 61 ASP cc_start: 0.8401 (m-30) cc_final: 0.8080 (m-30) REVERT: E 75 LYS cc_start: 0.8255 (ptpp) cc_final: 0.8026 (tptp) REVERT: E 88 ILE cc_start: 0.8709 (mm) cc_final: 0.8425 (mt) REVERT: F 54 GLU cc_start: 0.7307 (pp20) cc_final: 0.7086 (pp20) REVERT: F 91 GLN cc_start: 0.8495 (pm20) cc_final: 0.8188 (pm20) outliers start: 53 outliers final: 30 residues processed: 282 average time/residue: 0.1390 time to fit residues: 56.9289 Evaluate side-chains 242 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 206 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.154319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110558 restraints weight = 29217.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.112131 restraints weight = 15897.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113501 restraints weight = 10716.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113879 restraints weight = 8462.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114278 restraints weight = 7966.913| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15945 Z= 0.195 Angle : 0.813 30.241 21847 Z= 0.402 Chirality : 0.048 0.216 2361 Planarity : 0.006 0.118 2644 Dihedral : 17.337 136.507 2702 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.66 % Favored : 93.29 % Rotamer: Outliers : 4.16 % Allowed : 18.32 % Favored : 77.52 % 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: -0.96 (0.19), residues: 1773 helix: 0.57 (0.17), residues: 844 sheet: -0.69 (0.41), residues: 140 loop : -2.01 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 336 TYR 0.028 0.002 TYR D 527 PHE 0.020 0.002 PHE B 407 TRP 0.014 0.002 TRP F 17 HIS 0.008 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (15941) covalent geometry : angle 0.75318 / 0.40 (21835) hydrogen bonds : bond 0.06585 / 4.28 ( 770) hydrogen bonds : angle 5.06423 / 3.62 ( 2169) metal coordination : bond 0.00992 / 0.64 ( 4) metal coordination : angle 13.05123 / 7.26 ( 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 298 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 236 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8789 (t0) cc_final: 0.8479 (t0) REVERT: A 140 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 232 TYR cc_start: 0.8431 (t80) cc_final: 0.8045 (t80) REVERT: A 256 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7364 (tt0) REVERT: A 349 GLU cc_start: 0.7065 (mp0) cc_final: 0.6811 (mp0) REVERT: A 454 ARG cc_start: 0.6584 (ptp90) cc_final: 0.6274 (ptp90) REVERT: A 479 MET cc_start: 0.7343 (ttm) cc_final: 0.6952 (ttm) REVERT: A 526 LYS cc_start: 0.8571 (mttm) cc_final: 0.8217 (mptt) REVERT: B 351 LYS cc_start: 0.7545 (tptt) cc_final: 0.7161 (tptt) REVERT: B 389 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7275 (mm110) REVERT: B 555 ASN cc_start: 0.7083 (m110) cc_final: 0.6715 (m110) REVERT: C 227 GLN cc_start: 0.8517 (pp30) cc_final: 0.7954 (pt0) REVERT: C 280 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7787 (pp20) REVERT: C 291 TRP cc_start: 0.7127 (t-100) cc_final: 0.6579 (t60) REVERT: C 336 ARG cc_start: 0.7643 (mmp80) cc_final: 0.7422 (mmm160) REVERT: C 373 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7360 (pp) REVERT: C 389 GLN cc_start: 0.7624 (mp10) cc_final: 0.7180 (mp10) REVERT: C 465 MET cc_start: 0.8173 (ttm) cc_final: 0.7242 (ttm) REVERT: C 517 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6813 (tp30) REVERT: D 301 HIS cc_start: 0.7580 (p-80) cc_final: 0.7246 (p90) REVERT: D 344 ARG cc_start: 0.6688 (mtp180) cc_final: 0.4952 (mpt90) REVERT: D 358 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5585 (ttp) REVERT: D 379 ILE cc_start: 0.2899 (OUTLIER) cc_final: 0.2602 (tp) REVERT: D 394 MET cc_start: 0.4555 (mmt) cc_final: 0.3943 (mmt) REVERT: D 429 MET cc_start: 0.5983 (mmt) cc_final: 0.4238 (ptp) REVERT: D 430 LEU cc_start: 0.5746 (mt) cc_final: 0.5300 (mp) REVERT: D 478 LEU cc_start: 0.3624 (pp) cc_final: 0.3387 (pp) REVERT: E 2 GLU cc_start: 0.8072 (tt0) cc_final: 0.7790 (tt0) REVERT: E 9 TYR cc_start: 0.8589 (p90) cc_final: 0.8283 (p90) REVERT: E 22 LYS cc_start: 0.9015 (pptt) cc_final: 0.8679 (pttt) REVERT: E 61 ASP cc_start: 0.8532 (m-30) cc_final: 0.8175 (m-30) REVERT: E 88 ILE cc_start: 0.8919 (mm) cc_final: 0.8641 (mt) REVERT: F 91 GLN cc_start: 0.8401 (pm20) cc_final: 0.7958 (pm20) outliers start: 62 outliers final: 33 residues processed: 272 average time/residue: 0.1287 time to fit residues: 51.1178 Evaluate side-chains 242 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL 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: 20.0000 chunk 173 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN B 295 HIS B 366 HIS C 312 GLN D 538 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.152622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.106022 restraints weight = 28324.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109545 restraints weight = 14146.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.111955 restraints weight = 9323.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.113401 restraints weight = 7189.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114395 restraints weight = 6149.610| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15945 Z= 0.169 Angle : 0.757 21.752 21847 Z= 0.378 Chirality : 0.046 0.198 2361 Planarity : 0.006 0.117 2644 Dihedral : 17.082 136.855 2695 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.56 % Allowed : 19.80 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 1773 helix: 0.85 (0.18), residues: 844 sheet: -0.69 (0.41), residues: 145 loop : -1.92 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 336 TYR 0.022 0.002 TYR B 387 PHE 0.014 0.001 PHE D 391 TRP 0.024 0.002 TRP D 327 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (15941) covalent geometry : angle 0.71960 / 0.38 (21835) hydrogen bonds : bond 0.06269 / 4.05 ( 770) hydrogen bonds : angle 4.86289 / 3.46 ( 2169) metal coordination : bond 0.00718 / 0.44 ( 4) metal coordination : angle 10.04770 / 6.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8802 (t0) cc_final: 0.8527 (t0) REVERT: A 69 HIS cc_start: 0.8051 (t70) cc_final: 0.7670 (t70) REVERT: A 120 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: A 256 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7360 (tt0) REVERT: A 349 GLU cc_start: 0.7130 (mp0) cc_final: 0.6691 (mp0) REVERT: A 351 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7393 (mmtt) REVERT: A 479 MET cc_start: 0.7295 (ttm) cc_final: 0.6952 (ttm) REVERT: A 526 LYS cc_start: 0.8633 (mttm) cc_final: 0.8261 (mptt) REVERT: A 536 GLU cc_start: 0.7670 (tt0) cc_final: 0.7254 (mt-10) REVERT: C 227 GLN cc_start: 0.8517 (pp30) cc_final: 0.7944 (pt0) REVERT: C 265 ASN cc_start: 0.8471 (m-40) cc_final: 0.7881 (t0) REVERT: C 280 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7825 (pp20) REVERT: C 291 TRP cc_start: 0.7022 (t-100) cc_final: 0.6562 (t60) REVERT: C 373 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7307 (pp) REVERT: C 430 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7141 (tt) REVERT: C 517 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6854 (tp30) REVERT: D 344 ARG cc_start: 0.6818 (mtp180) cc_final: 0.5163 (mpt90) REVERT: D 358 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5559 (ttp) REVERT: D 379 ILE cc_start: 0.2835 (OUTLIER) cc_final: 0.2536 (tp) REVERT: D 394 MET cc_start: 0.4908 (mmt) cc_final: 0.4327 (mmt) REVERT: D 429 MET cc_start: 0.5143 (mmt) cc_final: 0.4126 (ptp) REVERT: D 451 HIS cc_start: 0.3635 (OUTLIER) cc_final: 0.2467 (m-70) REVERT: E 22 LYS cc_start: 0.8943 (pptt) cc_final: 0.8709 (pttt) REVERT: E 61 ASP cc_start: 0.8539 (m-30) cc_final: 0.8147 (m-30) REVERT: E 88 ILE cc_start: 0.8967 (mm) cc_final: 0.8668 (mt) REVERT: F 75 LYS cc_start: 0.7404 (mtmm) cc_final: 0.7141 (mmmt) REVERT: F 91 GLN cc_start: 0.8566 (pm20) cc_final: 0.8039 (pm20) outliers start: 53 outliers final: 29 residues processed: 253 average time/residue: 0.1345 time to fit residues: 50.0301 Evaluate side-chains 229 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 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 541 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 430 LEU 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 379 ILE Chi-restraints excluded: chain D residue 451 HIS 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 55 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 22 LYS 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: 20.0000 chunk 69 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 94 optimal weight: 0.0060 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN C 312 GLN D 538 GLN ** 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 = 0.3937 r_free = 0.3937 target = 0.142391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.093394 restraints weight = 29048.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096679 restraints weight = 15316.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098920 restraints weight = 10416.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100298 restraints weight = 8223.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101015 restraints weight = 7120.092| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 15945 Z= 0.349 Angle : 0.921 21.492 21847 Z= 0.474 Chirality : 0.054 0.203 2361 Planarity : 0.007 0.117 2644 Dihedral : 17.279 135.667 2695 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.12 % Rotamer: Outliers : 4.83 % Allowed : 19.93 % Favored : 75.23 % 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: -1.02 (0.19), residues: 1773 helix: 0.57 (0.17), residues: 841 sheet: -1.14 (0.38), residues: 167 loop : -2.02 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 386 TYR 0.027 0.003 TYR C 527 PHE 0.027 0.003 PHE B 407 TRP 0.028 0.003 TRP F 30 HIS 0.065 0.003 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.35 (15941) covalent geometry : angle 0.89336 / 0.47 (21835) hydrogen bonds : bond 0.07626 / 5.08 ( 770) hydrogen bonds : angle 5.22603 / 3.71 ( 2169) metal coordination : bond 0.01429 / 0.84 ( 4) metal coordination : angle 9.52747 / 5.36 ( 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 275 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 203 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9310 (mp) cc_final: 0.9081 (mp) REVERT: A 15 MET cc_start: 0.8604 (tpp) cc_final: 0.8247 (mmm) REVERT: A 105 LYS cc_start: 0.8446 (mttm) cc_final: 0.7997 (mtmm) REVERT: A 120 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: A 256 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7520 (tt0) REVERT: A 358 MET cc_start: 0.7816 (mmp) cc_final: 0.6368 (tmm) REVERT: A 361 GLN cc_start: 0.7993 (tt0) cc_final: 0.7405 (mm110) REVERT: A 429 MET cc_start: 0.9053 (tmm) cc_final: 0.8765 (tmm) REVERT: A 479 MET cc_start: 0.7540 (ttm) cc_final: 0.7103 (ttm) REVERT: A 516 MET cc_start: 0.8924 (mmm) cc_final: 0.7995 (mtp) REVERT: B 416 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7661 (mmtt) REVERT: C 227 GLN cc_start: 0.8685 (pp30) cc_final: 0.8061 (pt0) REVERT: C 280 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8056 (pp20) REVERT: C 291 TRP cc_start: 0.7315 (t-100) cc_final: 0.6860 (t60) REVERT: C 361 GLN cc_start: 0.9084 (mm110) cc_final: 0.8857 (mm110) REVERT: C 373 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7352 (pp) REVERT: C 465 MET cc_start: 0.8517 (ttm) cc_final: 0.7814 (ttm) REVERT: C 517 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7344 (tm-30) REVERT: D 285 TRP cc_start: 0.8089 (m100) cc_final: 0.7646 (m100) REVERT: D 301 HIS cc_start: 0.7635 (p-80) cc_final: 0.7180 (p90) REVERT: D 321 LEU cc_start: 0.5599 (mm) cc_final: 0.5285 (mt) REVERT: D 344 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6767 (mtp85) REVERT: D 358 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5615 (ttp) REVERT: D 362 ASP cc_start: 0.7762 (m-30) cc_final: 0.7522 (t70) REVERT: D 394 MET cc_start: 0.4843 (mmt) cc_final: 0.3279 (mmt) REVERT: D 431 THR cc_start: 0.6320 (p) cc_final: 0.5782 (p) REVERT: D 451 HIS cc_start: 0.3736 (OUTLIER) cc_final: 0.2809 (m-70) REVERT: E 22 LYS cc_start: 0.9119 (pptt) cc_final: 0.8842 (pttt) REVERT: E 39 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8535 (ttt-90) REVERT: F 1 MET cc_start: 0.7292 (tpp) cc_final: 0.6977 (tpp) REVERT: F 91 GLN cc_start: 0.8598 (pm20) cc_final: 0.8064 (pm20) outliers start: 72 outliers final: 37 residues processed: 255 average time/residue: 0.1542 time to fit residues: 55.1665 Evaluate side-chains 236 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 THR 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 488 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 B residue 233 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 280 GLU 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 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 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 451 HIS 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 39 ARG Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 54 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 17 optimal weight: 0.0370 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN C 334 ASN ** 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 = 0.3997 r_free = 0.3997 target = 0.147460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105312 restraints weight = 28849.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105100 restraints weight = 15831.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106158 restraints weight = 11176.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106738 restraints weight = 9473.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106924 restraints weight = 8422.556| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 15945 Z= 0.163 Angle : 0.745 14.805 21847 Z= 0.384 Chirality : 0.046 0.255 2361 Planarity : 0.005 0.059 2644 Dihedral : 17.150 138.384 2693 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.82 % Allowed : 22.28 % Favored : 74.90 % 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: -0.60 (0.20), residues: 1773 helix: 1.04 (0.18), residues: 834 sheet: -1.20 (0.37), residues: 182 loop : -1.88 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 412 TYR 0.020 0.002 TYR A 21 PHE 0.018 0.001 PHE D 391 TRP 0.021 0.002 TRP D 327 HIS 0.011 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (15941) covalent geometry : angle 0.72386 / 0.38 (21835) hydrogen bonds : bond 0.06541 / 4.29 ( 770) hydrogen bonds : angle 4.76981 / 3.39 ( 2169) metal coordination : bond 0.00377 / 0.23 ( 4) metal coordination : angle 7.51436 / 4.70 ( 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 249 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9306 (mp) cc_final: 0.9067 (mp) REVERT: A 105 LYS cc_start: 0.8413 (mttm) cc_final: 0.7944 (mtmm) REVERT: A 120 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: A 256 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7405 (tt0) REVERT: A 358 MET cc_start: 0.7752 (mmp) cc_final: 0.6282 (tmm) REVERT: A 479 MET cc_start: 0.7452 (ttm) cc_final: 0.7002 (ttm) REVERT: A 485 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7526 (mt-10) REVERT: A 516 MET cc_start: 0.8965 (mmm) cc_final: 0.7929 (mtp) REVERT: A 536 GLU cc_start: 0.7913 (tt0) cc_final: 0.7335 (mt-10) REVERT: B 351 LYS cc_start: 0.7636 (tptt) cc_final: 0.7110 (tptt) REVERT: C 227 GLN cc_start: 0.8703 (pp30) cc_final: 0.8017 (pt0) REVERT: C 291 TRP cc_start: 0.7337 (t-100) cc_final: 0.6810 (t60) REVERT: C 361 GLN cc_start: 0.9016 (mm110) cc_final: 0.8747 (mm-40) REVERT: C 465 MET cc_start: 0.8355 (ttm) cc_final: 0.7750 (ttm) REVERT: D 230 LYS cc_start: 0.5421 (OUTLIER) cc_final: 0.4132 (tppt) REVERT: D 301 HIS cc_start: 0.7762 (p-80) cc_final: 0.7338 (p90) REVERT: D 358 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5629 (ttp) REVERT: D 362 ASP cc_start: 0.7848 (m-30) cc_final: 0.7545 (t70) REVERT: D 394 MET cc_start: 0.4146 (mmt) cc_final: 0.3004 (mmt) REVERT: D 429 MET cc_start: 0.5775 (mmp) cc_final: 0.4740 (mtp) REVERT: D 434 TRP cc_start: 0.6963 (m100) cc_final: 0.6560 (m100) REVERT: D 451 HIS cc_start: 0.3832 (OUTLIER) cc_final: 0.2756 (m-70) REVERT: E 22 LYS cc_start: 0.9028 (pptt) cc_final: 0.8789 (pttt) REVERT: E 61 ASP cc_start: 0.8518 (m-30) cc_final: 0.8067 (m-30) REVERT: F 1 MET cc_start: 0.7630 (tpp) cc_final: 0.7357 (tpp) REVERT: F 49 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7550 (mt-10) REVERT: F 91 GLN cc_start: 0.8591 (pm20) cc_final: 0.8158 (pm20) REVERT: F 93 VAL cc_start: 0.9243 (m) cc_final: 0.9037 (p) outliers start: 42 outliers final: 26 residues processed: 231 average time/residue: 0.1347 time to fit residues: 44.7611 Evaluate side-chains 214 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 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 254 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 478 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 360 LEU Chi-restraints excluded: chain D residue 365 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 13 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 144 optimal weight: 0.0010 chunk 26 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN C 312 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.147948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105784 restraints weight = 29026.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105442 restraints weight = 15705.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106982 restraints weight = 10943.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107233 restraints weight = 9253.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108337 restraints weight = 8399.173| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15945 Z= 0.152 Angle : 0.722 14.532 21847 Z= 0.372 Chirality : 0.045 0.217 2361 Planarity : 0.005 0.058 2644 Dihedral : 16.897 137.901 2688 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.68 % Allowed : 23.22 % Favored : 74.09 % 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: -0.43 (0.20), residues: 1773 helix: 1.20 (0.18), residues: 832 sheet: -1.09 (0.38), residues: 182 loop : -1.81 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 19 TYR 0.016 0.001 TYR B 545 PHE 0.027 0.001 PHE B 407 TRP 0.021 0.002 TRP D 327 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15941) covalent geometry : angle 0.70428 / 0.37 (21835) hydrogen bonds : bond 0.06199 / 4.03 ( 770) hydrogen bonds : angle 4.66704 / 3.31 ( 2169) metal coordination : bond 0.00402 / 0.25 ( 4) metal coordination : angle 6.81510 / 4.54 ( 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 234 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9301 (mp) cc_final: 0.9080 (mp) REVERT: A 105 LYS cc_start: 0.8357 (mttm) cc_final: 0.7924 (mtmm) REVERT: A 120 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: A 256 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7351 (tt0) REVERT: A 358 MET cc_start: 0.7726 (mmp) cc_final: 0.6390 (tmm) REVERT: A 479 MET cc_start: 0.7527 (ttm) cc_final: 0.7114 (ttm) REVERT: A 485 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7548 (mt-10) REVERT: A 516 MET cc_start: 0.8957 (mmm) cc_final: 0.7986 (mtp) REVERT: A 526 LYS cc_start: 0.8769 (mttm) cc_final: 0.8341 (pttm) REVERT: A 536 GLU cc_start: 0.7941 (tt0) cc_final: 0.7364 (mt-10) REVERT: C 227 GLN cc_start: 0.8760 (pp30) cc_final: 0.8065 (pt0) REVERT: C 291 TRP cc_start: 0.7336 (t-100) cc_final: 0.6791 (t60) REVERT: C 361 GLN cc_start: 0.9035 (mm110) cc_final: 0.8816 (mm-40) REVERT: C 465 MET cc_start: 0.8398 (ttm) cc_final: 0.7739 (ttm) REVERT: C 518 GLN cc_start: 0.7220 (tp-100) cc_final: 0.6941 (tp40) REVERT: D 230 LYS cc_start: 0.5397 (OUTLIER) cc_final: 0.4130 (tppt) REVERT: D 301 HIS cc_start: 0.7725 (p-80) cc_final: 0.7301 (p90) REVERT: D 358 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5532 (ttp) REVERT: D 362 ASP cc_start: 0.7825 (m-30) cc_final: 0.7484 (t70) REVERT: D 394 MET cc_start: 0.4139 (mmt) cc_final: 0.3639 (mmt) REVERT: D 429 MET cc_start: 0.5937 (mmp) cc_final: 0.4852 (ptp) REVERT: D 451 HIS cc_start: 0.3802 (OUTLIER) cc_final: 0.2751 (m-70) REVERT: D 465 MET cc_start: 0.3694 (ptm) cc_final: 0.3368 (ptm) REVERT: E 22 LYS cc_start: 0.9027 (pptt) cc_final: 0.8701 (pttt) REVERT: E 61 ASP cc_start: 0.8450 (m-30) cc_final: 0.7996 (m-30) REVERT: F 1 MET cc_start: 0.7441 (tpp) cc_final: 0.7144 (tpp) REVERT: F 49 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7520 (mt-10) REVERT: F 91 GLN cc_start: 0.8596 (pm20) cc_final: 0.8149 (pm20) REVERT: F 93 VAL cc_start: 0.9247 (m) cc_final: 0.9040 (p) outliers start: 40 outliers final: 26 residues processed: 219 average time/residue: 0.1325 time to fit residues: 42.6891 Evaluate side-chains 213 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE 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 488 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 506 LYS 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 377 LEU Chi-restraints excluded: chain C residue 478 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 365 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 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 99 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 155 optimal weight: 30.0000 chunk 51 optimal weight: 0.2980 chunk 169 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.149470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101534 restraints weight = 28821.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105121 restraints weight = 14503.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107295 restraints weight = 9645.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.108944 restraints weight = 7606.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109691 restraints weight = 6512.841| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.7066 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= 0.141 Angle : 0.706 14.339 21847 Z= 0.364 Chirality : 0.044 0.162 2361 Planarity : 0.005 0.055 2644 Dihedral : 16.783 138.508 2686 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.42 % Allowed : 23.49 % Favored : 74.09 % 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: -0.35 (0.20), residues: 1773 helix: 1.26 (0.18), residues: 841 sheet: -0.97 (0.38), residues: 182 loop : -1.81 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 19 TYR 0.015 0.001 TYR A 21 PHE 0.020 0.001 PHE D 391 TRP 0.023 0.002 TRP D 327 HIS 0.005 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (15941) covalent geometry : angle 0.69087 / 0.36 (21835) hydrogen bonds : bond 0.05816 / 3.74 ( 770) hydrogen bonds : angle 4.55396 / 3.23 ( 2169) metal coordination : bond 0.00349 / 0.21 ( 4) metal coordination : angle 6.18151 / 4.56 ( 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 242 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.716 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: 0.9271 (mp) cc_final: 0.9053 (mp) REVERT: A 105 LYS cc_start: 0.8267 (mttm) cc_final: 0.7927 (mtmm) REVERT: A 256 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7355 (tt0) REVERT: A 358 MET cc_start: 0.7661 (mmp) cc_final: 0.6399 (tmm) REVERT: A 479 MET cc_start: 0.7537 (ttm) cc_final: 0.7228 (ttm) REVERT: A 485 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7517 (mt-10) REVERT: A 516 MET cc_start: 0.8983 (mmm) cc_final: 0.8050 (mtp) REVERT: A 526 LYS cc_start: 0.8774 (mttm) cc_final: 0.8304 (pttm) REVERT: A 536 GLU cc_start: 0.7780 (tt0) cc_final: 0.7337 (mt-10) REVERT: C 227 GLN cc_start: 0.8667 (pp30) cc_final: 0.7966 (pt0) REVERT: C 291 TRP cc_start: 0.7228 (t-100) cc_final: 0.6662 (t60) REVERT: C 518 GLN cc_start: 0.7123 (tp-100) cc_final: 0.6799 (tp40) REVERT: D 230 LYS cc_start: 0.5408 (OUTLIER) cc_final: 0.4102 (tppt) REVERT: D 259 GLN cc_start: 0.5324 (pm20) cc_final: 0.5053 (pm20) REVERT: D 301 HIS cc_start: 0.7649 (p-80) cc_final: 0.6795 (p90) REVERT: D 305 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8082 (mt-10) REVERT: D 358 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5586 (ttp) REVERT: D 362 ASP cc_start: 0.7773 (m-30) cc_final: 0.7496 (t70) REVERT: D 394 MET cc_start: 0.4570 (mmt) cc_final: 0.3831 (mmt) REVERT: D 429 MET cc_start: 0.5529 (mmp) cc_final: 0.4519 (ptp) REVERT: D 444 ASP cc_start: 0.7316 (t0) cc_final: 0.7019 (t0) REVERT: D 451 HIS cc_start: 0.3683 (OUTLIER) cc_final: 0.2758 (m-70) REVERT: E 61 ASP cc_start: 0.8445 (m-30) cc_final: 0.8087 (m-30) REVERT: F 49 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7523 (mt-10) REVERT: F 75 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7528 (mmmt) REVERT: F 91 GLN cc_start: 0.8609 (pm20) cc_final: 0.8011 (pm20) REVERT: F 93 VAL cc_start: 0.9200 (m) cc_final: 0.8983 (p) outliers start: 36 outliers final: 22 residues processed: 226 average time/residue: 0.1322 time to fit residues: 44.2028 Evaluate side-chains 215 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 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 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 478 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 365 ARG 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 F residue 13 ASN Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 124 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 137 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN D 538 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.148762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106246 restraints weight = 29061.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105516 restraints weight = 15632.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107702 restraints weight = 10569.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107990 restraints weight = 8368.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108084 restraints weight = 7856.792| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.7140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15945 Z= 0.158 Angle : 0.723 14.245 21847 Z= 0.370 Chirality : 0.045 0.183 2361 Planarity : 0.005 0.068 2644 Dihedral : 16.780 138.458 2686 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.15 % Allowed : 24.50 % Favored : 73.36 % 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: -0.39 (0.20), residues: 1773 helix: 1.19 (0.18), residues: 849 sheet: -0.96 (0.38), residues: 182 loop : -1.84 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 336 TYR 0.013 0.001 TYR D 527 PHE 0.019 0.001 PHE D 391 TRP 0.027 0.002 TRP D 434 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (15941) covalent geometry : angle 0.70767 / 0.37 (21835) hydrogen bonds : bond 0.05862 / 3.77 ( 770) hydrogen bonds : angle 4.55771 / 3.23 ( 2169) metal coordination : bond 0.00504 / 0.29 ( 4) metal coordination : angle 6.33553 / 4.51 ( 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 226 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.586 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: 0.9294 (mp) cc_final: 0.9079 (mp) REVERT: A 105 LYS cc_start: 0.8289 (mttm) cc_final: 0.7892 (mtmm) REVERT: A 256 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7373 (tt0) REVERT: A 351 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7074 (mmtt) REVERT: A 358 MET cc_start: 0.7740 (mmp) cc_final: 0.6420 (tmm) REVERT: A 479 MET cc_start: 0.7595 (ttm) cc_final: 0.7231 (ttm) REVERT: A 485 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7572 (mt-10) REVERT: A 516 MET cc_start: 0.9004 (mmm) cc_final: 0.8026 (mtp) REVERT: A 526 LYS cc_start: 0.8793 (mttm) cc_final: 0.8333 (pttm) REVERT: A 536 GLU cc_start: 0.7734 (tt0) cc_final: 0.7237 (mt-10) REVERT: C 227 GLN cc_start: 0.8694 (pp30) cc_final: 0.8002 (pt0) REVERT: C 291 TRP cc_start: 0.7297 (t-100) cc_final: 0.6774 (t60) REVERT: C 358 MET cc_start: 0.8791 (ppp) cc_final: 0.8371 (ppp) REVERT: C 465 MET cc_start: 0.8301 (ttm) cc_final: 0.7653 (ttm) REVERT: C 518 GLN cc_start: 0.7288 (tp-100) cc_final: 0.6995 (tp40) REVERT: D 230 LYS cc_start: 0.5408 (OUTLIER) cc_final: 0.4124 (tptt) REVERT: D 259 GLN cc_start: 0.5606 (pm20) cc_final: 0.5299 (pm20) REVERT: D 301 HIS cc_start: 0.7672 (p-80) cc_final: 0.7224 (p90) REVERT: D 358 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5536 (ttp) REVERT: D 362 ASP cc_start: 0.7864 (m-30) cc_final: 0.7562 (t70) REVERT: D 394 MET cc_start: 0.4127 (mmt) cc_final: 0.3588 (mmt) REVERT: D 429 MET cc_start: 0.5643 (mmp) cc_final: 0.4765 (mtm) REVERT: D 434 TRP cc_start: 0.7023 (m100) cc_final: 0.6765 (m100) REVERT: D 444 ASP cc_start: 0.7358 (t0) cc_final: 0.7089 (t0) REVERT: D 451 HIS cc_start: 0.4032 (OUTLIER) cc_final: 0.2976 (m-70) REVERT: D 538 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7465 (pp30) REVERT: E 61 ASP cc_start: 0.8494 (m-30) cc_final: 0.8105 (m-30) REVERT: F 75 LYS cc_start: 0.7817 (mmmt) cc_final: 0.7545 (mmmt) REVERT: F 91 GLN cc_start: 0.8589 (pm20) cc_final: 0.8020 (pm20) outliers start: 32 outliers final: 19 residues processed: 214 average time/residue: 0.1325 time to fit residues: 42.1083 Evaluate side-chains 209 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 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 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 365 ARG Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 538 GLN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 77 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.147839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105931 restraints weight = 28436.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106865 restraints weight = 15158.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108184 restraints weight = 10273.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108956 restraints weight = 8088.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109068 restraints weight = 7287.274| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15945 Z= 0.163 Angle : 0.725 14.069 21847 Z= 0.371 Chirality : 0.045 0.240 2361 Planarity : 0.005 0.053 2644 Dihedral : 16.801 137.659 2686 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.08 % Allowed : 24.43 % Favored : 73.49 % 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: -0.37 (0.20), residues: 1773 helix: 1.21 (0.18), residues: 849 sheet: -0.98 (0.38), residues: 182 loop : -1.83 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 340 TYR 0.014 0.001 TYR B 545 PHE 0.020 0.001 PHE D 391 TRP 0.021 0.002 TRP D 434 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (15941) covalent geometry : angle 0.70955 / 0.37 (21835) hydrogen bonds : bond 0.05919 / 3.82 ( 770) hydrogen bonds : angle 4.58716 / 3.26 ( 2169) metal coordination : bond 0.00500 / 0.29 ( 4) metal coordination : angle 6.45943 / 4.52 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3027.19 seconds wall clock time: 53 minutes 2.00 seconds (3182.00 seconds total)