Starting phenix.real_space_refine on Sat Jun 29 04:47:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rv2_19522/06_2024/8rv2_19522_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rv2_19522/06_2024/8rv2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rv2_19522/06_2024/8rv2_19522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rv2_19522/06_2024/8rv2_19522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rv2_19522/06_2024/8rv2_19522_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rv2_19522/06_2024/8rv2_19522_updated.pdb" } 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 Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "E TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 790": "OE1" <-> "OE2" Residue "F TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 8.57, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 6.56 Conformation dependent library (CDL) restraints added in 3.0 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... running ksdssp... Secondary structure from input PDB file: 113 helices and 18 sheets defined 50.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 137 through 145 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 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.629A pdb=" N ASP A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 195 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 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 223 through 232 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 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.530A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 335 through 346 removed outlier: 5.038A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.578A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 362 No H-bonds generated for 'chain 'A' and resid 359 through 362' Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.716A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 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 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 193 Processing helix chain 'B' and resid 204 through 216 removed outlier: 3.945A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 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 256 removed outlier: 3.533A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.774A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 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 338 through 348 removed outlier: 3.588A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 359 through 365 removed outlier: 4.170A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 373 removed outlier: 4.275A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 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 144 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.621A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 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 223 through 232 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 253 through 256 No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 removed outlier: 3.544A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 293 No H-bonds generated for 'chain 'C' and resid 290 through 293' Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.551A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.508A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 359 through 370 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) Proline residue: C 367 - end of helix removed outlier: 5.104A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.519A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.663A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 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 145 removed outlier: 3.699A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 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) removed outlier: 4.413A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 216 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 223 through 232 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.672A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 256' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 287 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 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 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 335 through 348 removed outlier: 3.587A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 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) Processing helix chain 'D' and resid 359 through 362 No H-bonds generated for 'chain 'D' and resid 359 through 362' Processing helix chain 'D' and resid 367 through 370 Processing helix chain 'E' and resid 583 through 587 Processing helix chain 'E' and resid 599 through 604 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) No H-bonds generated for 'chain 'E' and resid 599 through 604' Processing helix chain 'E' and resid 635 through 646 removed outlier: 3.549A pdb=" N LYS E 646 " --> pdb=" O ASN E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 661 removed outlier: 3.950A pdb=" N ALA E 657 " --> pdb=" O GLU E 653 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET E 658 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE E 659 " --> pdb=" O VAL E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 677 Processing helix chain 'E' and resid 682 through 690 Processing helix chain 'E' and resid 700 through 710 removed outlier: 3.705A pdb=" N TYR E 705 " --> pdb=" O ALA E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 750 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 753 through 768 removed outlier: 3.544A pdb=" N PHE E 767 " --> pdb=" O ARG E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 782 through 787 removed outlier: 3.722A pdb=" N LEU E 785 " --> pdb=" O ILE E 782 " (cutoff:3.500A) Processing helix chain 'E' and resid 800 through 810 removed outlier: 3.892A pdb=" N LYS E 810 " --> pdb=" O GLU E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 821 No H-bonds generated for 'chain 'E' and resid 818 through 821' Processing helix chain 'E' and resid 823 through 828 Processing helix chain 'E' and resid 833 through 856 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 859 through 896 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 907 through 932 Processing helix chain 'F' and resid 583 through 587 Processing helix chain 'F' and resid 599 through 605 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) Processing helix chain 'F' and resid 635 through 647 removed outlier: 3.645A pdb=" N ASN F 640 " --> pdb=" O LYS F 636 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN F 647 " --> pdb=" O ILE F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 661 Processing helix chain 'F' and resid 669 through 677 Processing helix chain 'F' and resid 682 through 690 removed outlier: 3.503A pdb=" N GLU F 686 " --> pdb=" O LYS F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 710 removed outlier: 3.867A pdb=" N TYR F 705 " --> pdb=" O ALA F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 749 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 753 through 768 Processing helix chain 'F' and resid 782 through 790 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) Processing helix chain 'F' and resid 800 through 810 removed outlier: 3.958A pdb=" N LYS F 810 " --> pdb=" O GLU F 806 " (cutoff:3.500A) Processing helix chain 'F' and resid 818 through 821 No H-bonds generated for 'chain 'F' and resid 818 through 821' Processing helix chain 'F' and resid 823 through 827 Processing helix chain 'F' and resid 833 through 855 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 859 through 896 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 907 through 932 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 297 through 300 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) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'B' and resid 132 through 136 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) removed outlier: 6.862A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.506A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.394A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= I, 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= J, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.964A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.670A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 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) Processing sheet with id= M, 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= N, first strand: chain 'D' and resid 132 through 136 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) removed outlier: 6.664A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= P, first strand: chain 'D' and resid 163 through 165 Processing sheet with id= Q, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.912A pdb=" N ASN D 162 " --> pdb=" O MET D 176 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 238 through 241 650 hydrogen bonds defined for protein. 1713 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: 5.30 Time building geometry restraints manager: 7.23 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: 99.17 - 107.28: 667 107.28 - 115.39: 10743 115.39 - 123.50: 11984 123.50 - 131.61: 384 131.61 - 139.72: 29 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: 123 2.59 - 3.17: 14263 3.17 - 3.75: 26417 3.75 - 4.32: 36378 4.32 - 4.90: 59959 Nonbonded interactions: 137140 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 2.440 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 2.440 nonbonded pdb=" OE2 GLU D 117 " pdb=" NE2 HIS D 371 " model vdw 2.242 2.520 ... (remaining 137135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 3.590 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: 10.200 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.080 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.080 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.940 ------------------------------------------------------------------------------- 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= 0.123 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 fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 2.103 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: 0.2420 time to fit residues: 57.3741 Evaluate side-chains 136 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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: 0.5980 chunk 163 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 888 GLN E 927 ASN ** F 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 888 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17583 Z= 0.283 Angle : 0.569 7.210 23807 Z= 0.285 Chirality : 0.044 0.175 2680 Planarity : 0.005 0.039 3045 Dihedral : 7.219 136.484 2426 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.95 % Allowed : 18.99 % Favored : 78.06 % 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: -0.08 (0.18), residues: 2146 helix: 0.17 (0.16), residues: 1062 sheet: 0.29 (0.35), residues: 226 loop : -0.23 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 569 HIS 0.005 0.001 HIS A 101 PHE 0.014 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 196 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 141 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8386 (ptt90) REVERT: D 207 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7837 (mm-30) outliers start: 55 outliers final: 32 residues processed: 185 average time/residue: 0.2442 time to fit residues: 73.1328 Evaluate side-chains 169 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 ILE 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 56 ASP Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 149 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 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 103 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain F residue 705 TYR Chi-restraints excluded: chain F residue 706 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 175 optimal weight: 0.5980 chunk 194 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 864 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17583 Z= 0.345 Angle : 0.587 10.514 23807 Z= 0.293 Chirality : 0.045 0.160 2680 Planarity : 0.005 0.041 3045 Dihedral : 6.877 115.757 2424 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.86 % Allowed : 19.05 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.18), residues: 2146 helix: 0.18 (0.16), residues: 1062 sheet: 0.03 (0.34), residues: 232 loop : -0.55 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 569 HIS 0.005 0.001 HIS A 161 PHE 0.017 0.001 PHE B 255 TYR 0.015 0.002 TYR E 865 ARG 0.003 0.000 ARG C 196 *********************** 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 211 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 139 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8416 (ptt90) REVERT: B 252 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: C 236 LEU cc_start: 0.7868 (tp) cc_final: 0.7611 (tt) REVERT: D 207 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7904 (mm-30) outliers start: 72 outliers final: 46 residues processed: 203 average time/residue: 0.2429 time to fit residues: 80.4914 Evaluate side-chains 176 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 127 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 ILE 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 56 ASP Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 252 ASN 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 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 110 LEU 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 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 207 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 663 ASP 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 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 194 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 208 optimal weight: 30.0000 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17583 Z= 0.287 Angle : 0.550 7.692 23807 Z= 0.274 Chirality : 0.043 0.186 2680 Planarity : 0.005 0.070 3045 Dihedral : 6.599 117.750 2424 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.08 % Allowed : 19.10 % Favored : 76.82 % 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: -0.28 (0.18), residues: 2146 helix: 0.27 (0.16), residues: 1060 sheet: -0.14 (0.34), residues: 232 loop : -0.61 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 569 HIS 0.005 0.001 HIS A 161 PHE 0.015 0.001 PHE B 255 TYR 0.012 0.001 TYR B 69 ARG 0.002 0.000 ARG B 147 *********************** 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 213 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 137 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 TYR cc_start: 0.7382 (m-80) cc_final: 0.7127 (m-80) REVERT: B 50 LYS cc_start: 0.7734 (mmtt) cc_final: 0.6612 (pttm) REVERT: B 62 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8369 (ptt90) REVERT: C 236 LEU cc_start: 0.7833 (tp) cc_final: 0.7616 (tt) REVERT: D 207 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7931 (mm-30) outliers start: 76 outliers final: 56 residues processed: 205 average time/residue: 0.2417 time to fit residues: 80.2649 Evaluate side-chains 189 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 131 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 201 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 ILE 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 56 ASP 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 149 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 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 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 207 GLU Chi-restraints excluded: chain D residue 286 ASP 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 663 ASP Chi-restraints excluded: chain E residue 732 ASP 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 927 ASN Chi-restraints excluded: chain F residue 598 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 864 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 17583 Z= 0.377 Angle : 0.606 8.848 23807 Z= 0.304 Chirality : 0.046 0.234 2680 Planarity : 0.005 0.054 3045 Dihedral : 6.609 116.958 2424 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 4.67 % Allowed : 19.58 % Favored : 75.75 % 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: -0.55 (0.18), residues: 2146 helix: 0.19 (0.16), residues: 1053 sheet: -0.65 (0.33), residues: 242 loop : -0.83 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.005 0.001 HIS A 161 PHE 0.018 0.001 PHE B 255 TYR 0.017 0.002 TYR E 865 ARG 0.003 0.000 ARG E 763 *********************** 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 221 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 134 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7998 (ttm) REVERT: A 283 MET cc_start: 0.8125 (mmm) cc_final: 0.7818 (mtm) REVERT: B 50 LYS cc_start: 0.7659 (mmtt) cc_final: 0.6549 (pttm) REVERT: B 62 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8454 (ptt90) REVERT: C 171 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8305 (mp) REVERT: C 236 LEU cc_start: 0.7849 (tp) cc_final: 0.7618 (tt) REVERT: D 207 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8021 (mm-30) REVERT: D 236 LEU cc_start: 0.6930 (mt) cc_final: 0.6710 (tp) REVERT: D 244 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7164 (p0) REVERT: E 705 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.5979 (m-10) REVERT: E 854 VAL cc_start: 0.9048 (m) cc_final: 0.8819 (p) REVERT: F 721 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6351 (pmm) outliers start: 87 outliers final: 69 residues processed: 210 average time/residue: 0.2360 time to fit residues: 80.9828 Evaluate side-chains 203 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 127 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 304 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 56 ASP 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 149 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 277 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 286 ASP 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 B residue 358 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 56 ASP 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 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 207 GLU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 ASP 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 663 ASP Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 718 ILE Chi-restraints excluded: chain E residue 732 ASP 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 789 THR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 927 ASN Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 598 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 30.0000 chunk 173 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 0.0370 chunk 109 optimal weight: 3.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- 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 ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 115 ASN ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1919 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= 0.208 Angle : 0.522 8.300 23807 Z= 0.258 Chirality : 0.042 0.200 2680 Planarity : 0.004 0.046 3045 Dihedral : 6.318 111.046 2424 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Rotamer: Outliers : 3.70 % Allowed : 21.24 % Favored : 75.05 % 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: -0.16 (0.19), residues: 2146 helix: 0.49 (0.17), residues: 1027 sheet: -0.53 (0.32), residues: 254 loop : -0.55 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.004 0.001 HIS A 161 PHE 0.012 0.001 PHE C 31 TYR 0.015 0.001 TYR E 865 ARG 0.001 0.000 ARG B 183 *********************** 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 199 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 130 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7108 (mtmm) REVERT: A 132 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7913 (ttm) REVERT: B 50 LYS cc_start: 0.7653 (mmtt) cc_final: 0.6643 (pttm) REVERT: C 171 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8214 (mp) REVERT: D 207 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: D 299 MET cc_start: 0.7722 (mmt) cc_final: 0.7331 (mmt) REVERT: E 854 VAL cc_start: 0.9056 (m) cc_final: 0.8833 (p) outliers start: 69 outliers final: 53 residues processed: 191 average time/residue: 0.2407 time to fit residues: 75.0523 Evaluate side-chains 182 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 125 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 VAL 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 358 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP 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 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 207 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 ASP 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 663 ASP Chi-restraints excluded: chain E residue 718 ILE Chi-restraints excluded: chain E residue 732 ASP Chi-restraints excluded: chain E residue 745 CYS Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 927 ASN Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 705 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 175 optimal weight: 0.0020 chunk 116 optimal weight: 0.6980 chunk 208 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 115 ASN ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 864 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17583 Z= 0.184 Angle : 0.522 10.439 23807 Z= 0.256 Chirality : 0.041 0.216 2680 Planarity : 0.004 0.043 3045 Dihedral : 6.145 103.336 2424 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.44 % Rotamer: Outliers : 3.54 % Allowed : 21.35 % Favored : 75.11 % 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: -0.03 (0.19), residues: 2146 helix: 0.56 (0.17), residues: 1045 sheet: -0.35 (0.32), residues: 266 loop : -0.50 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.005 0.001 HIS A 161 PHE 0.012 0.001 PHE C 31 TYR 0.015 0.001 TYR D 294 ARG 0.001 0.000 ARG F 717 *********************** 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 196 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 130 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7090 (mtmm) REVERT: A 132 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7941 (ttm) REVERT: B 50 LYS cc_start: 0.7677 (mmtt) cc_final: 0.6661 (pttm) REVERT: C 171 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8180 (mp) REVERT: D 207 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: E 854 VAL cc_start: 0.9065 (m) cc_final: 0.8846 (p) outliers start: 66 outliers final: 50 residues processed: 187 average time/residue: 0.2398 time to fit residues: 73.2706 Evaluate side-chains 181 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 127 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 149 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 358 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 LEU 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 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 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 663 ASP Chi-restraints excluded: chain E residue 718 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17583 Z= 0.237 Angle : 0.541 12.442 23807 Z= 0.267 Chirality : 0.043 0.232 2680 Planarity : 0.004 0.043 3045 Dihedral : 6.170 100.040 2424 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 3.86 % Allowed : 21.08 % Favored : 75.05 % 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: -0.08 (0.19), residues: 2146 helix: 0.55 (0.17), residues: 1045 sheet: -0.39 (0.32), residues: 266 loop : -0.55 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.005 0.001 HIS A 161 PHE 0.013 0.001 PHE B 255 TYR 0.016 0.001 TYR E 865 ARG 0.001 0.000 ARG D 62 *********************** 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 202 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 130 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7932 (ttm) REVERT: B 50 LYS cc_start: 0.7652 (mmtt) cc_final: 0.6645 (pttm) REVERT: C 171 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8181 (mp) REVERT: D 207 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7920 (mm-30) REVERT: E 705 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6045 (m-10) REVERT: E 854 VAL cc_start: 0.9070 (m) cc_final: 0.8854 (p) outliers start: 72 outliers final: 60 residues processed: 195 average time/residue: 0.2306 time to fit residues: 73.5890 Evaluate side-chains 191 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 127 time to evaluate : 1.754 ------------------------------------------------------------------------------- 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 132 MET 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 282 ILE Chi-restraints excluded: chain A residue 304 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 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 149 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 358 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 LEU 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 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 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 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 326 LYS Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 718 ILE Chi-restraints excluded: chain E residue 732 ASP 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 927 ASN Chi-restraints excluded: chain F residue 598 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 50.0000 chunk 181 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17583 Z= 0.171 Angle : 0.518 13.475 23807 Z= 0.253 Chirality : 0.041 0.217 2680 Planarity : 0.004 0.044 3045 Dihedral : 6.024 94.634 2424 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.19 % Favored : 97.76 % Rotamer: Outliers : 3.59 % Allowed : 21.62 % Favored : 74.79 % 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: 0.10 (0.19), residues: 2146 helix: 0.66 (0.17), residues: 1047 sheet: -0.28 (0.32), residues: 266 loop : -0.43 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 356 HIS 0.005 0.001 HIS A 161 PHE 0.012 0.001 PHE C 31 TYR 0.015 0.001 TYR E 865 ARG 0.001 0.000 ARG B 183 *********************** 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 197 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 130 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7108 (mtmm) REVERT: A 132 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7964 (ttm) REVERT: B 50 LYS cc_start: 0.7636 (mmtt) cc_final: 0.6663 (pttm) REVERT: D 207 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: D 299 MET cc_start: 0.7688 (mmt) cc_final: 0.7287 (mmt) REVERT: E 705 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6008 (m-10) REVERT: E 854 VAL cc_start: 0.9068 (m) cc_final: 0.8811 (p) outliers start: 67 outliers final: 55 residues processed: 189 average time/residue: 0.2305 time to fit residues: 71.8332 Evaluate side-chains 187 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 128 time to evaluate : 1.933 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 304 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 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 149 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 351 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 THR 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 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 207 GLU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 ASP 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 663 ASP Chi-restraints excluded: chain E residue 705 TYR Chi-restraints excluded: chain E residue 718 ILE Chi-restraints excluded: chain E residue 732 ASP 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 F residue 598 ASP Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 705 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 215 optimal weight: 7.9990 chunk 198 optimal weight: 0.0000 chunk 171 optimal weight: 0.0010 chunk 17 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.4980 chunk 136 optimal weight: 0.8980 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17583 Z= 0.125 Angle : 0.498 13.290 23807 Z= 0.242 Chirality : 0.040 0.193 2680 Planarity : 0.004 0.044 3045 Dihedral : 5.826 86.612 2424 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.31 % Allowed : 23.18 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.19), residues: 2146 helix: 0.83 (0.17), residues: 1038 sheet: -0.14 (0.33), residues: 242 loop : -0.22 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 356 HIS 0.004 0.000 HIS A 161 PHE 0.012 0.001 PHE C 31 TYR 0.015 0.001 TYR E 865 ARG 0.001 0.000 ARG B 183 ********************** 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 173 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.8500 (t) cc_final: 0.8185 (p) REVERT: A 118 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7095 (mtmm) REVERT: B 50 LYS cc_start: 0.7712 (mmtt) cc_final: 0.6759 (pttm) REVERT: D 113 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8318 (mmmm) REVERT: D 207 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: D 299 MET cc_start: 0.7686 (mmt) cc_final: 0.7288 (mmt) outliers start: 43 outliers final: 34 residues processed: 168 average time/residue: 0.2574 time to fit residues: 70.3837 Evaluate side-chains 167 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 203 THR 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 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 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 56 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 LEU 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 D residue 6 THR 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 286 ASP 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 663 ASP Chi-restraints excluded: chain E residue 718 ILE Chi-restraints excluded: chain E residue 732 ASP Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 697 LYS Chi-restraints excluded: chain F residue 705 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 171 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.158063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121576 restraints weight = 26463.303| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.49 r_work: 0.3302 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17583 Z= 0.146 Angle : 0.505 13.889 23807 Z= 0.244 Chirality : 0.040 0.195 2680 Planarity : 0.004 0.044 3045 Dihedral : 5.789 81.879 2424 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.04 % Allowed : 23.44 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.17), residues: 1040 sheet: -0.00 (0.34), residues: 244 loop : -0.21 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 356 HIS 0.011 0.001 HIS E 703 PHE 0.011 0.001 PHE C 31 TYR 0.014 0.001 TYR D 294 ARG 0.001 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3099.95 seconds wall clock time: 56 minutes 34.59 seconds (3394.59 seconds total)