Starting phenix.real_space_refine on Tue Jan 21 19:27:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rv2_19522/01_2025/8rv2_19522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rv2_19522/01_2025/8rv2_19522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rv2_19522/01_2025/8rv2_19522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rv2_19522/01_2025/8rv2_19522.map" model { file = "/net/cci-nas-00/data/ceres_data/8rv2_19522/01_2025/8rv2_19522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rv2_19522/01_2025/8rv2_19522.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 110 5.16 5 C 10884 2.51 5 N 2932 2.21 5 O 3308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17248 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2776 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 2 Chain: "F" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2776 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 11, 'TRANS': 336} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.76, per 1000 atoms: 0.62 Number of scatterers: 17248 At special positions: 0 Unit cell: (115.2, 126.9, 182.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 10 15.00 Mg 4 11.99 O 3308 8.00 N 2932 7.00 C 10884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 2.2 seconds 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 24 sheets defined 57.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.719A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.159A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.586A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.546A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.813A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.527A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.572A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.714A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.589A pdb=" N ASP A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.903A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.684A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.781A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.791A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.630A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.602A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 203 through 217 removed outlier: 3.956A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.934A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.869A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.616A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.871A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.678A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.588A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.816A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 4.170A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.982A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.830A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.621A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.832A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 234 through 237 removed outlier: 3.543A pdb=" N GLU C 237 " --> pdb=" O SER C 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 237' Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.882A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.544A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.589A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.604A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.551A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.513A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.669A pdb=" N ASP C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.872A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.663A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.749A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.609A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.629A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 217 removed outlier: 3.751A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.691A pdb=" N ARG D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 257' Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.005A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.981A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.563A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 349 through 356 removed outlier: 3.847A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 366 through 371 removed outlier: 3.522A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 588 removed outlier: 4.213A pdb=" N SER E 586 " --> pdb=" O SER E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 605 removed outlier: 3.760A pdb=" N GLU E 603 " --> pdb=" O PHE E 599 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 604 " --> pdb=" O SER E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 645 Processing helix chain 'E' and resid 651 through 656 Processing helix chain 'E' and resid 656 through 662 Processing helix chain 'E' and resid 668 through 678 Processing helix chain 'E' and resid 681 through 691 Processing helix chain 'E' and resid 699 through 711 removed outlier: 3.705A pdb=" N TYR E 705 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 711 " --> pdb=" O LEU E 707 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 751 removed outlier: 3.581A pdb=" N GLU E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET E 721 " --> pdb=" O ARG E 717 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 726 " --> pdb=" O LEU E 722 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 729 " --> pdb=" O GLU E 725 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 731 " --> pdb=" O ALA E 727 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP E 732 " --> pdb=" O ALA E 728 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET E 733 " --> pdb=" O ALA E 729 " (cutoff:3.500A) Proline residue: E 736 - end of helix Processing helix chain 'E' and resid 752 through 769 removed outlier: 3.933A pdb=" N ILE E 756 " --> pdb=" O ARG E 752 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE E 767 " --> pdb=" O ARG E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 788 removed outlier: 3.722A pdb=" N LEU E 785 " --> pdb=" O ILE E 782 " (cutoff:3.500A) Processing helix chain 'E' and resid 799 through 809 Processing helix chain 'E' and resid 817 through 822 removed outlier: 3.653A pdb=" N ASP E 821 " --> pdb=" O GLN E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 829 Processing helix chain 'E' and resid 832 through 857 removed outlier: 4.078A pdb=" N ILE E 836 " --> pdb=" O ASN E 832 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER E 838 " --> pdb=" O GLU E 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS E 853 " --> pdb=" O GLU E 849 " (cutoff:3.500A) Processing helix chain 'E' and resid 858 through 897 removed outlier: 4.234A pdb=" N GLN E 864 " --> pdb=" O GLU E 860 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU E 867 " --> pdb=" O GLU E 863 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG E 868 " --> pdb=" O GLN E 864 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG E 877 " --> pdb=" O ILE E 873 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA E 878 " --> pdb=" O SER E 874 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 879 " --> pdb=" O ALA E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 906 through 933 Processing helix chain 'F' and resid 583 through 588 removed outlier: 3.856A pdb=" N LEU F 587 " --> pdb=" O MET F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 606 removed outlier: 3.751A pdb=" N GLU F 603 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG F 604 " --> pdb=" O SER F 600 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE F 606 " --> pdb=" O ILE F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 646 removed outlier: 3.645A pdb=" N ASN F 640 " --> pdb=" O LYS F 636 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 662 Processing helix chain 'F' and resid 668 through 678 Processing helix chain 'F' and resid 681 through 691 removed outlier: 3.503A pdb=" N GLU F 686 " --> pdb=" O LYS F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 711 removed outlier: 3.867A pdb=" N TYR F 705 " --> pdb=" O ALA F 701 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE F 711 " --> pdb=" O LEU F 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 750 removed outlier: 3.680A pdb=" N GLU F 719 " --> pdb=" O GLN F 715 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET F 721 " --> pdb=" O ARG F 717 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS F 724 " --> pdb=" O CYS F 720 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP F 732 " --> pdb=" O ALA F 728 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET F 733 " --> pdb=" O ALA F 729 " (cutoff:3.500A) Proline residue: F 736 - end of helix Processing helix chain 'F' and resid 752 through 769 removed outlier: 3.703A pdb=" N ILE F 756 " --> pdb=" O ARG F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 791 removed outlier: 3.597A pdb=" N LEU F 785 " --> pdb=" O ILE F 782 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 788 " --> pdb=" O LEU F 785 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR F 789 " --> pdb=" O LEU F 786 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR F 791 " --> pdb=" O LEU F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 799 through 811 removed outlier: 3.958A pdb=" N LYS F 810 " --> pdb=" O GLU F 806 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER F 811 " --> pdb=" O GLU F 807 " (cutoff:3.500A) Processing helix chain 'F' and resid 817 through 822 removed outlier: 3.641A pdb=" N ASP F 821 " --> pdb=" O GLN F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 828 Processing helix chain 'F' and resid 832 through 856 removed outlier: 4.142A pdb=" N ILE F 836 " --> pdb=" O ASN F 832 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 852 " --> pdb=" O LEU F 848 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS F 853 " --> pdb=" O GLU F 849 " (cutoff:3.500A) Processing helix chain 'F' and resid 858 through 897 removed outlier: 3.666A pdb=" N GLN F 862 " --> pdb=" O VAL F 858 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN F 864 " --> pdb=" O GLU F 860 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU F 867 " --> pdb=" O GLU F 863 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG F 868 " --> pdb=" O GLN F 864 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG F 877 " --> pdb=" O ILE F 873 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 878 " --> pdb=" O SER F 874 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU F 879 " --> pdb=" O ALA F 875 " (cutoff:3.500A) Processing helix chain 'F' and resid 906 through 933 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.332A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.446A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.984A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.506A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.105A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.705A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.774A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.670A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.428A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.515A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 250 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.662A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.503A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.912A pdb=" N ASN D 162 " --> pdb=" O MET D 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.240A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 829 hydrogen bonds defined for protein. 2238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5659 1.34 - 1.46: 2986 1.46 - 1.58: 8738 1.58 - 1.69: 14 1.69 - 1.81: 186 Bond restraints: 17583 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" CA MET B 47 " pdb=" CB MET B 47 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.33e-02 5.65e+03 8.34e-01 bond pdb=" CA GLY D 20 " pdb=" C GLY D 20 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.20e-02 6.94e+03 7.22e-01 ... (remaining 17578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 23416 1.44 - 2.87: 274 2.87 - 4.31: 78 4.31 - 5.74: 32 5.74 - 7.18: 7 Bond angle restraints: 23807 Sorted by residual: angle pdb=" N GLY D 20 " pdb=" CA GLY D 20 " pdb=" C GLY D 20 " ideal model delta sigma weight residual 110.20 113.66 -3.46 1.32e+00 5.74e-01 6.89e+00 angle pdb=" CB MET F 564 " pdb=" CG MET F 564 " pdb=" SD MET F 564 " ideal model delta sigma weight residual 112.70 119.88 -7.18 3.00e+00 1.11e-01 5.73e+00 angle pdb=" N VAL B 201 " pdb=" CA VAL B 201 " pdb=" C VAL B 201 " ideal model delta sigma weight residual 106.42 109.68 -3.26 1.51e+00 4.39e-01 4.65e+00 angle pdb=" O1B ADP A 401 " pdb=" PB ADP A 401 " pdb=" O2B ADP A 401 " ideal model delta sigma weight residual 119.90 113.64 6.26 3.00e+00 1.11e-01 4.35e+00 angle pdb=" O1B ADP C 401 " pdb=" PB ADP C 401 " pdb=" O2B ADP C 401 " ideal model delta sigma weight residual 119.90 113.70 6.20 3.00e+00 1.11e-01 4.27e+00 ... (remaining 23802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 10361 35.17 - 70.35: 338 70.35 - 105.52: 30 105.52 - 140.70: 1 140.70 - 175.87: 2 Dihedral angle restraints: 10732 sinusoidal: 4386 harmonic: 6346 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.87 -175.87 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.99 -162.98 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 168.77 131.23 1 2.00e+01 2.50e-03 3.98e+01 ... (remaining 10729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1715 0.030 - 0.061: 673 0.061 - 0.091: 145 0.091 - 0.121: 143 0.121 - 0.151: 4 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CA GLN F 864 " pdb=" N GLN F 864 " pdb=" C GLN F 864 " pdb=" CB GLN F 864 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE E 711 " pdb=" N ILE E 711 " pdb=" C ILE E 711 " pdb=" CB ILE E 711 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 2677 not shown) Planarity restraints: 3045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 334 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C GLU B 334 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU B 334 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 335 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 572 " -0.025 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO F 573 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 573 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 573 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 572 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO E 573 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 573 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 573 " 0.021 5.00e-02 4.00e+02 ... (remaining 3042 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 122 2.59 - 3.17: 14145 3.17 - 3.75: 26288 3.75 - 4.32: 36012 4.32 - 4.90: 59881 Nonbonded interactions: 136448 Sorted by model distance: nonbonded pdb=" O1G ATP D 401 " pdb="MG MG D 402 " model vdw 2.017 2.170 nonbonded pdb=" O ILE A 122 " pdb=" OG1 THR A 126 " model vdw 2.163 3.040 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.206 2.170 nonbonded pdb=" OG1 THR C 358 " pdb=" OE1 GLU C 361 " model vdw 2.221 3.040 nonbonded pdb=" OE2 GLU D 117 " pdb=" NE2 HIS D 371 " model vdw 2.242 3.120 ... (remaining 136443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 374 or resid 402)) selection = (chain 'B' and (resid 5 through 374 or resid 402)) selection = (chain 'C' and (resid 5 through 374 or resid 402)) selection = (chain 'D' and (resid 5 through 374 or resid 402)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.620 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.002 0.023 17583 Z= 0.120 Angle : 0.470 7.180 23807 Z= 0.228 Chirality : 0.039 0.151 2680 Planarity : 0.003 0.039 3045 Dihedral : 17.140 175.869 6628 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.05 % Allowed : 19.96 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2146 helix: -0.00 (0.16), residues: 1020 sheet: 0.49 (0.36), residues: 202 loop : 0.07 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 569 HIS 0.006 0.001 HIS C 371 PHE 0.008 0.001 PHE B 255 TYR 0.012 0.001 TYR F 865 ARG 0.002 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 145 average time/residue: 0.2616 time to fit residues: 61.9147 Evaluate side-chains 136 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 126 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 115 ASN E 888 GLN E 927 ASN F 888 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.163525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.125844 restraints weight = 26199.227| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.84 r_work: 0.3328 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17583 Z= 0.251 Angle : 0.577 6.818 23807 Z= 0.295 Chirality : 0.044 0.173 2680 Planarity : 0.005 0.038 3045 Dihedral : 6.997 137.635 2426 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.58 % Allowed : 18.94 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2146 helix: 0.51 (0.16), residues: 1052 sheet: 0.57 (0.34), residues: 232 loop : 0.02 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 569 HIS 0.006 0.001 HIS A 101 PHE 0.012 0.001 PHE B 255 TYR 0.016 0.001 TYR A 198 ARG 0.003 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.8729 (t) cc_final: 0.8525 (p) REVERT: B 62 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8428 (ptt90) REVERT: C 132 MET cc_start: 0.8374 (tmm) cc_final: 0.8023 (ttm) REVERT: C 354 GLN cc_start: 0.7203 (mp10) cc_final: 0.6768 (pp30) REVERT: D 207 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8046 (mm-30) outliers start: 48 outliers final: 25 residues processed: 179 average time/residue: 0.2574 time to fit residues: 75.5589 Evaluate side-chains 159 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain F residue 705 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 23 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN C 111 ASN C 115 ASN F 864 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.160320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.124873 restraints weight = 26195.858| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.71 r_work: 0.3289 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17583 Z= 0.383 Angle : 0.621 8.318 23807 Z= 0.316 Chirality : 0.046 0.179 2680 Planarity : 0.005 0.041 3045 Dihedral : 6.713 118.382 2424 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 3.33 % Allowed : 18.56 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2146 helix: 0.45 (0.16), residues: 1056 sheet: 0.22 (0.34), residues: 232 loop : -0.45 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 79 HIS 0.019 0.002 HIS A 101 PHE 0.017 0.002 PHE B 255 TYR 0.015 0.002 TYR D 294 ARG 0.003 0.000 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 138 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8411 (mp) REVERT: C 236 LEU cc_start: 0.7909 (tp) cc_final: 0.7675 (tt) REVERT: D 207 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8088 (mm-30) outliers start: 62 outliers final: 46 residues processed: 195 average time/residue: 0.2548 time to fit residues: 80.6067 Evaluate side-chains 177 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 789 THR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 927 ASN Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain F residue 706 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 163 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 156 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 115 ASN ** F 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.163859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.127021 restraints weight = 26014.040| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.71 r_work: 0.3361 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17583 Z= 0.156 Angle : 0.508 6.406 23807 Z= 0.254 Chirality : 0.041 0.165 2680 Planarity : 0.004 0.038 3045 Dihedral : 6.302 118.046 2424 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.58 % Allowed : 19.47 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2146 helix: 0.79 (0.17), residues: 1056 sheet: 0.26 (0.33), residues: 244 loop : -0.21 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 356 HIS 0.007 0.001 HIS A 101 PHE 0.010 0.001 PHE C 31 TYR 0.013 0.001 TYR E 865 ARG 0.003 0.000 ARG E 877 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.7504 (mmtt) cc_final: 0.6469 (pttm) REVERT: D 207 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7981 (mm-30) outliers start: 48 outliers final: 31 residues processed: 179 average time/residue: 0.2507 time to fit residues: 72.8627 Evaluate side-chains 163 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain F residue 706 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 139 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 115 ASN F 864 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.160244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.125214 restraints weight = 26338.254| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.69 r_work: 0.3298 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17583 Z= 0.351 Angle : 0.602 12.112 23807 Z= 0.303 Chirality : 0.046 0.235 2680 Planarity : 0.005 0.043 3045 Dihedral : 6.449 119.030 2424 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.92 % Allowed : 18.29 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2146 helix: 0.72 (0.17), residues: 1044 sheet: -0.20 (0.32), residues: 254 loop : -0.37 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 79 HIS 0.005 0.001 HIS A 161 PHE 0.016 0.001 PHE B 255 TYR 0.016 0.002 TYR A 198 ARG 0.003 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 132 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 50 LYS cc_start: 0.7581 (mmtt) cc_final: 0.6498 (pttm) REVERT: C 171 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8229 (mp) REVERT: D 207 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: F 721 MET cc_start: 0.6599 (pmm) cc_final: 0.6274 (pmm) outliers start: 73 outliers final: 57 residues processed: 198 average time/residue: 0.2573 time to fit residues: 82.4959 Evaluate side-chains 189 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 129 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 745 CYS Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain F residue 706 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 159 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 864 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.163512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.124243 restraints weight = 26161.222| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.92 r_work: 0.3302 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17583 Z= 0.166 Angle : 0.524 10.562 23807 Z= 0.261 Chirality : 0.041 0.201 2680 Planarity : 0.004 0.042 3045 Dihedral : 6.148 111.629 2424 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.95 % Allowed : 19.64 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2146 helix: 0.92 (0.17), residues: 1048 sheet: -0.04 (0.33), residues: 232 loop : -0.20 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 356 HIS 0.004 0.001 HIS A 161 PHE 0.011 0.001 PHE C 31 TYR 0.014 0.001 TYR E 865 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7121 (mtmm) REVERT: B 50 LYS cc_start: 0.7601 (mmtt) cc_final: 0.6519 (pttm) REVERT: D 207 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7988 (mm-30) REVERT: F 721 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6419 (pmm) outliers start: 55 outliers final: 38 residues processed: 184 average time/residue: 0.2545 time to fit residues: 76.1065 Evaluate side-chains 172 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain F residue 721 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 183 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 78 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN F 864 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.158111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126972 restraints weight = 26351.011| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.60 r_work: 0.3331 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 17583 Z= 0.473 Angle : 0.682 9.510 23807 Z= 0.346 Chirality : 0.049 0.244 2680 Planarity : 0.006 0.055 3045 Dihedral : 6.659 114.647 2424 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.76 % Rotamer: Outliers : 3.65 % Allowed : 19.69 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2146 helix: 0.48 (0.17), residues: 1061 sheet: -0.59 (0.31), residues: 256 loop : -0.68 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 79 HIS 0.006 0.001 HIS D 275 PHE 0.019 0.002 PHE B 255 TYR 0.021 0.002 TYR E 865 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 127 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8577 (mp) REVERT: B 50 LYS cc_start: 0.7501 (mmtt) cc_final: 0.6452 (pttm) REVERT: D 207 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: F 721 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6387 (pmm) outliers start: 68 outliers final: 58 residues processed: 185 average time/residue: 0.2612 time to fit residues: 77.8072 Evaluate side-chains 188 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 127 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 789 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 927 ASN Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain F residue 721 MET Chi-restraints excluded: chain F residue 865 TYR Chi-restraints excluded: chain F residue 909 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 177 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 864 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.162111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.125647 restraints weight = 26018.512| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.80 r_work: 0.3296 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17583 Z= 0.182 Angle : 0.544 8.865 23807 Z= 0.272 Chirality : 0.042 0.218 2680 Planarity : 0.004 0.047 3045 Dihedral : 6.255 106.658 2424 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.00 % Allowed : 20.60 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 2146 helix: 0.78 (0.17), residues: 1059 sheet: -0.14 (0.32), residues: 256 loop : -0.40 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 86 HIS 0.004 0.001 HIS A 161 PHE 0.011 0.001 PHE C 31 TYR 0.012 0.001 TYR B 69 ARG 0.002 0.000 ARG E 877 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7190 (mtmm) REVERT: B 50 LYS cc_start: 0.7529 (mmtt) cc_final: 0.6470 (pttm) REVERT: D 207 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8024 (mm-30) REVERT: F 721 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6550 (pmm) outliers start: 56 outliers final: 48 residues processed: 178 average time/residue: 0.2574 time to fit residues: 73.9358 Evaluate side-chains 178 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain F residue 721 MET Chi-restraints excluded: chain F residue 730 VAL Chi-restraints excluded: chain F residue 865 TYR Chi-restraints excluded: chain F residue 909 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 129 optimal weight: 0.2980 chunk 176 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 864 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.159018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.126800 restraints weight = 26424.354| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.68 r_work: 0.3310 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 17583 Z= 0.411 Angle : 0.652 11.854 23807 Z= 0.329 Chirality : 0.047 0.248 2680 Planarity : 0.005 0.055 3045 Dihedral : 6.510 106.677 2424 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.33 % Allowed : 20.01 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2146 helix: 0.57 (0.17), residues: 1058 sheet: -0.61 (0.31), residues: 258 loop : -0.70 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 86 HIS 0.005 0.001 HIS D 275 PHE 0.017 0.002 PHE B 255 TYR 0.013 0.002 TYR C 218 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 50 LYS cc_start: 0.7549 (mmtt) cc_final: 0.6498 (pttm) REVERT: D 207 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: F 721 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6443 (pmm) outliers start: 62 outliers final: 55 residues processed: 182 average time/residue: 0.2532 time to fit residues: 74.5053 Evaluate side-chains 185 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 127 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain F residue 721 MET Chi-restraints excluded: chain F residue 730 VAL Chi-restraints excluded: chain F residue 865 TYR Chi-restraints excluded: chain F residue 909 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 29 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 200 optimal weight: 50.0000 chunk 173 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 211 optimal weight: 30.0000 chunk 102 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 766 ASN F 864 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.161037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.125779 restraints weight = 26193.904| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.65 r_work: 0.3313 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17583 Z= 0.209 Angle : 0.561 12.799 23807 Z= 0.281 Chirality : 0.043 0.223 2680 Planarity : 0.005 0.052 3045 Dihedral : 6.226 99.182 2424 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.95 % Allowed : 20.60 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 2146 helix: 0.77 (0.17), residues: 1056 sheet: -0.25 (0.32), residues: 256 loop : -0.44 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 86 HIS 0.005 0.001 HIS A 161 PHE 0.012 0.001 PHE B 255 TYR 0.012 0.001 TYR B 69 ARG 0.003 0.000 ARG B 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.7539 (mmtt) cc_final: 0.6485 (pttm) REVERT: D 207 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: F 721 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6671 (pmm) outliers start: 55 outliers final: 47 residues processed: 177 average time/residue: 0.2530 time to fit residues: 73.4100 Evaluate side-chains 178 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain F residue 721 MET Chi-restraints excluded: chain F residue 730 VAL Chi-restraints excluded: chain F residue 865 TYR Chi-restraints excluded: chain F residue 909 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 7 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 123 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.157730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.120106 restraints weight = 26245.563| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.12 r_work: 0.3253 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17583 Z= 0.161 Angle : 0.546 13.796 23807 Z= 0.270 Chirality : 0.041 0.213 2680 Planarity : 0.004 0.044 3045 Dihedral : 5.933 87.358 2424 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.31 % Allowed : 21.41 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 2146 helix: 0.93 (0.17), residues: 1059 sheet: -0.12 (0.34), residues: 232 loop : -0.29 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 86 HIS 0.004 0.001 HIS A 161 PHE 0.012 0.001 PHE C 31 TYR 0.014 0.001 TYR F 896 ARG 0.002 0.000 ARG E 877 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7324.43 seconds wall clock time: 131 minutes 22.01 seconds (7882.01 seconds total)