Starting phenix.real_space_refine on Sat Mar 16 17:04:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/03_2024/6lyp_30017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/03_2024/6lyp_30017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/03_2024/6lyp_30017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/03_2024/6lyp_30017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/03_2024/6lyp_30017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lyp_30017/03_2024/6lyp_30017.pdb" } resolution = 3.3 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= 0.011 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9744 2.51 5 N 2548 2.21 5 O 2793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "E ARG 257": "NH1" <-> "NH2" Residue "E ARG 265": "NH1" <-> "NH2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "F ARG 257": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F ARG 342": "NH1" <-> "NH2" Residue "F PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 444": "NH1" <-> "NH2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "G ARG 257": "NH1" <-> "NH2" Residue "G ARG 265": "NH1" <-> "NH2" Residue "G ARG 342": "NH1" <-> "NH2" Residue "G PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G ARG 460": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15169 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 7.37, per 1000 atoms: 0.49 Number of scatterers: 15169 At special positions: 0 Unit cell: (102.96, 100.88, 123.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2793 8.00 N 2548 7.00 C 9744 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: 5.36 Conformation dependent library (CDL) restraints added in 3.1 seconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3710 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 21 sheets defined 48.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.641A pdb=" N ALA A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.779A pdb=" N THR A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 327 through 342 removed outlier: 4.063A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.698A pdb=" N SER A 385 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.676A pdb=" N LYS A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.639A pdb=" N ALA B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.644A pdb=" N ILE B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.700A pdb=" N SER B 385 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 386' Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 474 " --> pdb=" O GLN B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.641A pdb=" N ALA C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 251 through 266 removed outlier: 4.493A pdb=" N ARG C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.643A pdb=" N ILE C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR C 312 " --> pdb=" O GLN C 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER C 385 " --> pdb=" O ASN C 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 386' Processing helix chain 'C' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 474 " --> pdb=" O GLN C 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 223 removed outlier: 3.640A pdb=" N ALA D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG D 257 " --> pdb=" O TRP D 253 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 262 " --> pdb=" O TRP D 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 282 removed outlier: 3.779A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR D 312 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER D 385 " --> pdb=" O ASN D 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 381 through 386' Processing helix chain 'D' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS D 422 " --> pdb=" O SER D 418 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 469 " --> pdb=" O GLU D 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 474 " --> pdb=" O GLN D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 223 removed outlier: 3.640A pdb=" N ALA E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG E 257 " --> pdb=" O TRP E 253 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 262 " --> pdb=" O TRP E 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE E 263 " --> pdb=" O LYS E 259 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 282 removed outlier: 3.779A pdb=" N THR E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 287 Processing helix chain 'E' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR E 312 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 324 Processing helix chain 'E' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER E 385 " --> pdb=" O ASN E 381 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 381 through 386' Processing helix chain 'E' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS E 422 " --> pdb=" O SER E 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 469 " --> pdb=" O GLU E 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 474 " --> pdb=" O GLN E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.641A pdb=" N ALA F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 251 through 266 removed outlier: 4.493A pdb=" N ARG F 257 " --> pdb=" O TRP F 253 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 262 " --> pdb=" O TRP F 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 Processing helix chain 'F' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR F 312 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 327 through 342 removed outlier: 4.063A pdb=" N GLN F 339 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE F 340 " --> pdb=" O LEU F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER F 385 " --> pdb=" O ASN F 381 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 381 through 386' Processing helix chain 'F' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS F 422 " --> pdb=" O SER F 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 469 " --> pdb=" O GLU F 465 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU F 474 " --> pdb=" O GLN F 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.640A pdb=" N ALA G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE G 220 " --> pdb=" O LEU G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG G 257 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL G 262 " --> pdb=" O TRP G 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 287 Processing helix chain 'G' and resid 289 through 303 removed outlier: 3.537A pdb=" N ILE G 294 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU G 301 " --> pdb=" O MET G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 removed outlier: 3.644A pdb=" N ILE G 310 " --> pdb=" O ALA G 306 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR G 312 " --> pdb=" O GLN G 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 313 " --> pdb=" O SER G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 324 Processing helix chain 'G' and resid 327 through 342 removed outlier: 4.063A pdb=" N GLN G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE G 340 " --> pdb=" O LEU G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER G 385 " --> pdb=" O ASN G 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER G 386 " --> pdb=" O SER G 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 381 through 386' Processing helix chain 'G' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS G 422 " --> pdb=" O SER G 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER G 427 " --> pdb=" O GLU G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN G 468 " --> pdb=" O GLU G 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR G 469 " --> pdb=" O GLU G 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU G 474 " --> pdb=" O GLN G 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 350 removed outlier: 6.682A pdb=" N SER A 368 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET A 362 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 389 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.650A pdb=" N ILE A 389 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET B 362 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER B 368 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR A 441 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER A 487 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.648A pdb=" N ILE B 389 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR C 366 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET C 362 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER C 368 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 399 through 401 removed outlier: 3.861A pdb=" N TYR B 441 " --> pdb=" O THR B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER B 487 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.626A pdb=" N ILE C 389 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR D 366 " --> pdb=" O MET D 362 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET D 362 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER D 368 " --> pdb=" O ILE D 360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR C 441 " --> pdb=" O THR C 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER C 487 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.637A pdb=" N ILE D 389 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET E 362 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER E 368 " --> pdb=" O ILE E 360 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 399 through 401 removed outlier: 3.861A pdb=" N TYR D 441 " --> pdb=" O THR D 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 406 through 407 removed outlier: 3.748A pdb=" N SER D 487 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 389 through 390 removed outlier: 7.202A pdb=" N THR F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET F 362 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER F 368 " --> pdb=" O ILE F 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR E 441 " --> pdb=" O THR E 453 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 406 through 407 removed outlier: 3.746A pdb=" N SER E 487 " --> pdb=" O GLN E 407 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 389 through 390 removed outlier: 3.561A pdb=" N ILE F 389 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR G 366 " --> pdb=" O MET G 362 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET G 362 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER G 368 " --> pdb=" O ILE G 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 399 through 401 removed outlier: 3.861A pdb=" N TYR F 441 " --> pdb=" O THR F 453 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER F 487 " --> pdb=" O GLN F 407 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR G 441 " --> pdb=" O THR G 453 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER G 487 " --> pdb=" O GLN G 407 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1743 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: 4.82 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2973 1.33 - 1.45: 3346 1.45 - 1.57: 8941 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 15407 Sorted by residual: bond pdb=" C PHE B 375 " pdb=" N PRO B 376 " ideal model delta sigma weight residual 1.334 1.205 0.129 2.34e-02 1.83e+03 3.05e+01 bond pdb=" C PHE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.334 1.205 0.129 2.34e-02 1.83e+03 3.02e+01 bond pdb=" C PHE E 375 " pdb=" N PRO E 376 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 3.01e+01 bond pdb=" C PHE C 375 " pdb=" N PRO C 376 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 3.00e+01 bond pdb=" C PHE F 375 " pdb=" N PRO F 376 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 3.00e+01 ... (remaining 15402 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.83: 447 106.83 - 113.94: 8795 113.94 - 121.06: 7404 121.06 - 128.17: 4102 128.17 - 135.28: 105 Bond angle restraints: 20853 Sorted by residual: angle pdb=" C LYS C 374 " pdb=" N PHE C 375 " pdb=" CA PHE C 375 " ideal model delta sigma weight residual 121.83 135.28 -13.45 1.56e+00 4.11e-01 7.43e+01 angle pdb=" C LYS D 374 " pdb=" N PHE D 375 " pdb=" CA PHE D 375 " ideal model delta sigma weight residual 121.83 135.26 -13.43 1.56e+00 4.11e-01 7.41e+01 angle pdb=" C LYS F 374 " pdb=" N PHE F 375 " pdb=" CA PHE F 375 " ideal model delta sigma weight residual 121.83 135.25 -13.42 1.56e+00 4.11e-01 7.40e+01 angle pdb=" C LYS E 374 " pdb=" N PHE E 375 " pdb=" CA PHE E 375 " ideal model delta sigma weight residual 121.83 135.23 -13.40 1.56e+00 4.11e-01 7.38e+01 angle pdb=" C LYS G 374 " pdb=" N PHE G 375 " pdb=" CA PHE G 375 " ideal model delta sigma weight residual 121.83 135.20 -13.37 1.56e+00 4.11e-01 7.35e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.59: 7795 10.59 - 21.17: 1081 21.17 - 31.76: 287 31.76 - 42.34: 105 42.34 - 52.93: 42 Dihedral angle restraints: 9310 sinusoidal: 3563 harmonic: 5747 Sorted by residual: dihedral pdb=" CA TRP E 253 " pdb=" C TRP E 253 " pdb=" N PHE E 254 " pdb=" CA PHE E 254 " ideal model delta harmonic sigma weight residual 180.00 149.23 30.77 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA TRP B 253 " pdb=" C TRP B 253 " pdb=" N PHE B 254 " pdb=" CA PHE B 254 " ideal model delta harmonic sigma weight residual 180.00 149.31 30.69 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA TRP G 253 " pdb=" C TRP G 253 " pdb=" N PHE G 254 " pdb=" CA PHE G 254 " ideal model delta harmonic sigma weight residual 180.00 149.33 30.67 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 9307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1556 0.059 - 0.117: 621 0.117 - 0.176: 283 0.176 - 0.234: 53 0.234 - 0.293: 14 Chirality restraints: 2527 Sorted by residual: chirality pdb=" CB ILE G 459 " pdb=" CA ILE G 459 " pdb=" CG1 ILE G 459 " pdb=" CG2 ILE G 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE F 459 " pdb=" CA ILE F 459 " pdb=" CG1 ILE F 459 " pdb=" CG2 ILE F 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE A 459 " pdb=" CA ILE A 459 " pdb=" CG1 ILE A 459 " pdb=" CG2 ILE A 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 2524 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 355 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C VAL F 355 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL F 355 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU F 356 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 355 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C VAL B 355 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL B 355 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 356 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 355 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" C VAL A 355 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL A 355 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 356 " 0.018 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 587 2.70 - 3.25: 14426 3.25 - 3.80: 23785 3.80 - 4.35: 31622 4.35 - 4.90: 51212 Nonbonded interactions: 121632 Sorted by model distance: nonbonded pdb=" OG1 THR A 491 " pdb=" OE2 GLU G 446 " model vdw 2.148 2.440 nonbonded pdb=" OE2 GLU C 446 " pdb=" OG1 THR D 491 " model vdw 2.215 2.440 nonbonded pdb=" OE2 GLU B 446 " pdb=" OG1 THR C 491 " model vdw 2.234 2.440 nonbonded pdb=" OE2 GLU F 446 " pdb=" OG1 THR G 491 " model vdw 2.249 2.440 nonbonded pdb=" OE2 GLU E 446 " pdb=" OG1 THR F 491 " model vdw 2.253 2.440 ... (remaining 121627 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.710 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: 4.030 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 41.080 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 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 : 0.011 0.129 15407 Z= 0.719 Angle : 1.350 13.450 20853 Z= 0.725 Chirality : 0.076 0.293 2527 Planarity : 0.007 0.046 2604 Dihedral : 11.789 52.927 5600 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 1.40 % Allowed : 11.54 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -6.19 (0.13), residues: 1995 helix: -4.35 (0.08), residues: 973 sheet: -2.72 (0.30), residues: 224 loop : -4.01 (0.18), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP C 397 HIS 0.004 0.002 HIS E 484 PHE 0.033 0.004 PHE A 323 TYR 0.033 0.005 TYR C 467 ARG 0.009 0.001 ARG F 398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 298 time to evaluate : 1.729 Fit side-chains REVERT: A 285 LYS cc_start: 0.7561 (ttmp) cc_final: 0.7151 (ttmm) REVERT: A 287 SER cc_start: 0.8504 (t) cc_final: 0.8234 (p) REVERT: B 266 MET cc_start: 0.5081 (ttm) cc_final: 0.4845 (ttp) REVERT: B 278 GLU cc_start: 0.6243 (mt-10) cc_final: 0.6039 (tt0) REVERT: B 285 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7232 (tttp) REVERT: B 287 SER cc_start: 0.8719 (t) cc_final: 0.8355 (p) REVERT: B 428 ASN cc_start: 0.7766 (t160) cc_final: 0.7544 (t0) REVERT: B 432 PHE cc_start: 0.6563 (t80) cc_final: 0.6113 (t80) REVERT: B 436 GLU cc_start: 0.7900 (mp0) cc_final: 0.7685 (mt-10) REVERT: C 266 MET cc_start: 0.5471 (ttm) cc_final: 0.5221 (ttp) REVERT: C 287 SER cc_start: 0.8635 (t) cc_final: 0.8251 (p) REVERT: D 287 SER cc_start: 0.8700 (t) cc_final: 0.8351 (p) REVERT: D 346 MET cc_start: 0.8005 (mmt) cc_final: 0.7769 (mmm) REVERT: D 360 ILE cc_start: 0.7778 (mt) cc_final: 0.7061 (mt) REVERT: D 432 PHE cc_start: 0.6604 (t80) cc_final: 0.6046 (t80) REVERT: E 266 MET cc_start: 0.5433 (ttm) cc_final: 0.5159 (ttp) REVERT: E 278 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6472 (tt0) REVERT: E 285 LYS cc_start: 0.7733 (ttmp) cc_final: 0.7282 (ttmt) REVERT: E 287 SER cc_start: 0.8567 (t) cc_final: 0.8203 (p) REVERT: E 346 MET cc_start: 0.7997 (mmt) cc_final: 0.7742 (mmm) REVERT: E 360 ILE cc_start: 0.8039 (mt) cc_final: 0.7673 (mt) REVERT: E 406 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6391 (pp) REVERT: E 429 THR cc_start: 0.7346 (p) cc_final: 0.7142 (p) REVERT: E 460 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6885 (tpt90) REVERT: E 467 TYR cc_start: 0.8143 (m-80) cc_final: 0.7792 (m-80) REVERT: F 266 MET cc_start: 0.5665 (ttm) cc_final: 0.5406 (ttp) REVERT: F 287 SER cc_start: 0.8537 (t) cc_final: 0.7907 (p) REVERT: F 346 MET cc_start: 0.7964 (mmt) cc_final: 0.7499 (mmm) REVERT: F 428 ASN cc_start: 0.7763 (t160) cc_final: 0.7466 (t0) REVERT: F 429 THR cc_start: 0.7074 (p) cc_final: 0.6774 (p) REVERT: F 446 GLU cc_start: 0.7117 (tt0) cc_final: 0.6873 (tt0) REVERT: F 474 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4909 (tp) REVERT: F 484 HIS cc_start: 0.7273 (m-70) cc_final: 0.6889 (m-70) REVERT: G 266 MET cc_start: 0.5724 (ttm) cc_final: 0.5471 (ttp) REVERT: G 278 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6328 (tp30) REVERT: G 285 LYS cc_start: 0.7752 (ttmp) cc_final: 0.7297 (tttp) REVERT: G 287 SER cc_start: 0.8673 (t) cc_final: 0.8151 (p) REVERT: G 346 MET cc_start: 0.7907 (mmt) cc_final: 0.7535 (mmm) REVERT: G 428 ASN cc_start: 0.7595 (t160) cc_final: 0.7385 (t0) REVERT: G 429 THR cc_start: 0.7283 (p) cc_final: 0.7013 (p) REVERT: G 436 GLU cc_start: 0.7708 (mp0) cc_final: 0.7345 (mt-10) REVERT: G 460 ARG cc_start: 0.6887 (tpt170) cc_final: 0.6673 (tpt90) outliers start: 23 outliers final: 0 residues processed: 316 average time/residue: 0.2915 time to fit residues: 130.7576 Evaluate side-chains 209 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 407 GLN B 358 GLN B 407 GLN B 428 ASN B 470 GLN C 358 GLN C 407 GLN C 470 GLN D 358 GLN D 470 GLN E 358 GLN E 407 GLN F 358 GLN F 407 GLN F 428 ASN G 358 GLN G 407 GLN G 428 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15407 Z= 0.221 Angle : 0.702 9.477 20853 Z= 0.366 Chirality : 0.047 0.158 2527 Planarity : 0.005 0.036 2604 Dihedral : 6.652 43.641 2118 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.88 % Allowed : 13.00 % Favored : 82.11 % 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: -5.16 (0.15), residues: 1995 helix: -3.04 (0.13), residues: 973 sheet: -1.92 (0.31), residues: 238 loop : -4.33 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 397 HIS 0.003 0.001 HIS G 484 PHE 0.012 0.002 PHE G 323 TYR 0.010 0.001 TYR G 467 ARG 0.003 0.000 ARG D 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 248 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.7340 (m) cc_final: 0.7035 (t) REVERT: A 287 SER cc_start: 0.8431 (t) cc_final: 0.7755 (p) REVERT: A 308 GLN cc_start: 0.7977 (pm20) cc_final: 0.7705 (pm20) REVERT: A 474 LEU cc_start: 0.5244 (OUTLIER) cc_final: 0.5014 (tt) REVERT: B 266 MET cc_start: 0.5050 (ttm) cc_final: 0.4707 (ttp) REVERT: B 278 GLU cc_start: 0.6341 (mt-10) cc_final: 0.6096 (tt0) REVERT: B 285 LYS cc_start: 0.7816 (ttmp) cc_final: 0.7299 (tttp) REVERT: B 287 SER cc_start: 0.8301 (t) cc_final: 0.7741 (p) REVERT: B 296 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7651 (tp) REVERT: B 308 GLN cc_start: 0.8102 (pm20) cc_final: 0.7819 (pm20) REVERT: B 378 LEU cc_start: 0.8296 (tt) cc_final: 0.8031 (mp) REVERT: B 413 MET cc_start: 0.5456 (tpp) cc_final: 0.5192 (mpp) REVERT: B 432 PHE cc_start: 0.6647 (t80) cc_final: 0.6381 (t80) REVERT: B 436 GLU cc_start: 0.7899 (mp0) cc_final: 0.7604 (mt-10) REVERT: B 474 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4974 (tt) REVERT: C 287 SER cc_start: 0.8284 (t) cc_final: 0.7696 (p) REVERT: C 308 GLN cc_start: 0.7941 (pm20) cc_final: 0.7689 (pm20) REVERT: C 447 LYS cc_start: 0.6927 (tppt) cc_final: 0.6701 (tppt) REVERT: D 287 SER cc_start: 0.8439 (t) cc_final: 0.7921 (p) REVERT: D 474 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5519 (tp) REVERT: E 278 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6599 (tt0) REVERT: E 285 LYS cc_start: 0.7637 (ttmp) cc_final: 0.7097 (ttmt) REVERT: E 287 SER cc_start: 0.8358 (t) cc_final: 0.7778 (p) REVERT: E 338 MET cc_start: 0.7306 (mmp) cc_final: 0.6829 (mmp) REVERT: E 413 MET cc_start: 0.5136 (tpp) cc_final: 0.4904 (mpp) REVERT: E 460 ARG cc_start: 0.7116 (tpt170) cc_final: 0.6854 (tpt90) REVERT: F 287 SER cc_start: 0.8250 (t) cc_final: 0.7610 (p) REVERT: F 292 PHE cc_start: 0.6791 (t80) cc_final: 0.6490 (t80) REVERT: F 346 MET cc_start: 0.7676 (mmt) cc_final: 0.7390 (mmm) REVERT: F 484 HIS cc_start: 0.6703 (m-70) cc_final: 0.6153 (m90) REVERT: G 266 MET cc_start: 0.5288 (ttm) cc_final: 0.5052 (ttp) REVERT: G 278 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6442 (tt0) REVERT: G 285 LYS cc_start: 0.7733 (ttmp) cc_final: 0.7186 (tttp) REVERT: G 287 SER cc_start: 0.8393 (t) cc_final: 0.7772 (p) REVERT: G 368 SER cc_start: 0.8966 (p) cc_final: 0.8599 (t) REVERT: G 378 LEU cc_start: 0.8162 (tt) cc_final: 0.7959 (mp) REVERT: G 417 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.6176 (mp) REVERT: G 436 GLU cc_start: 0.7742 (mp0) cc_final: 0.7406 (mt-10) REVERT: G 460 ARG cc_start: 0.7009 (tpt170) cc_final: 0.6727 (tpm170) outliers start: 80 outliers final: 41 residues processed: 311 average time/residue: 0.2442 time to fit residues: 113.9540 Evaluate side-chains 267 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 0.0770 chunk 192 optimal weight: 0.0670 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 60 optimal weight: 0.0020 chunk 143 optimal weight: 7.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN B 358 GLN B 470 GLN C 358 GLN C 457 ASN C 470 GLN D 339 GLN D 358 GLN D 484 HIS F 457 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15407 Z= 0.154 Angle : 0.621 8.222 20853 Z= 0.322 Chirality : 0.044 0.142 2527 Planarity : 0.004 0.027 2604 Dihedral : 5.739 33.692 2116 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.43 % Allowed : 14.10 % Favored : 80.46 % 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: -4.34 (0.16), residues: 1995 helix: -2.17 (0.15), residues: 973 sheet: -1.69 (0.32), residues: 238 loop : -4.16 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 397 HIS 0.002 0.001 HIS D 484 PHE 0.010 0.001 PHE D 375 TYR 0.008 0.001 TYR E 441 ARG 0.005 0.000 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 226 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6406 (tp30) cc_final: 0.5694 (mt-10) REVERT: A 287 SER cc_start: 0.8381 (t) cc_final: 0.7733 (p) REVERT: A 413 MET cc_start: 0.5236 (tpp) cc_final: 0.4991 (mpp) REVERT: A 474 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4788 (tt) REVERT: B 266 MET cc_start: 0.4595 (ttm) cc_final: 0.4374 (ttp) REVERT: B 287 SER cc_start: 0.8245 (t) cc_final: 0.7677 (p) REVERT: B 361 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7175 (mt-10) REVERT: B 432 PHE cc_start: 0.6367 (t80) cc_final: 0.6084 (t80) REVERT: C 278 GLU cc_start: 0.6422 (tp30) cc_final: 0.5845 (mt-10) REVERT: C 287 SER cc_start: 0.8304 (t) cc_final: 0.7720 (p) REVERT: C 361 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7012 (mt-10) REVERT: C 436 GLU cc_start: 0.7733 (mt-10) cc_final: 0.6772 (mp0) REVERT: D 278 GLU cc_start: 0.6727 (tp30) cc_final: 0.6011 (tt0) REVERT: D 287 SER cc_start: 0.8399 (t) cc_final: 0.7839 (p) REVERT: D 474 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5097 (tt) REVERT: D 484 HIS cc_start: 0.7023 (m-70) cc_final: 0.6563 (m90) REVERT: E 278 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6687 (tt0) REVERT: E 287 SER cc_start: 0.8350 (t) cc_final: 0.7778 (p) REVERT: E 338 MET cc_start: 0.7337 (mmp) cc_final: 0.6934 (mmp) REVERT: E 378 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7741 (mp) REVERT: E 460 ARG cc_start: 0.7110 (tpt170) cc_final: 0.6854 (tpt90) REVERT: F 287 SER cc_start: 0.8278 (t) cc_final: 0.7592 (p) REVERT: F 292 PHE cc_start: 0.6717 (t80) cc_final: 0.6470 (t80) REVERT: G 270 LYS cc_start: 0.5727 (OUTLIER) cc_final: 0.5432 (tmtt) REVERT: G 287 SER cc_start: 0.8411 (t) cc_final: 0.7749 (p) REVERT: G 297 MET cc_start: 0.8275 (ttm) cc_final: 0.7883 (ttm) REVERT: G 368 SER cc_start: 0.8696 (p) cc_final: 0.8451 (m) REVERT: G 413 MET cc_start: 0.5586 (tpp) cc_final: 0.5089 (mpp) REVERT: G 436 GLU cc_start: 0.7686 (mp0) cc_final: 0.7306 (mt-10) REVERT: G 460 ARG cc_start: 0.7029 (tpt170) cc_final: 0.6748 (tpm170) outliers start: 89 outliers final: 60 residues processed: 294 average time/residue: 0.2409 time to fit residues: 106.0692 Evaluate side-chains 260 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 196 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 457 ASN Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 92 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 470 GLN C 339 GLN C 470 GLN C 484 HIS E 358 GLN F 358 GLN G 358 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15407 Z= 0.326 Angle : 0.698 7.988 20853 Z= 0.359 Chirality : 0.048 0.147 2527 Planarity : 0.004 0.026 2604 Dihedral : 6.087 35.736 2116 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 7.33 % Allowed : 14.71 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.24 (0.17), residues: 1995 helix: -1.93 (0.16), residues: 966 sheet: -2.22 (0.31), residues: 266 loop : -4.15 (0.18), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 397 HIS 0.003 0.001 HIS C 484 PHE 0.013 0.002 PHE C 432 TYR 0.007 0.001 TYR C 467 ARG 0.005 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 214 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6434 (tp30) cc_final: 0.5693 (mt-10) REVERT: A 287 SER cc_start: 0.8555 (t) cc_final: 0.7871 (p) REVERT: A 474 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5109 (tt) REVERT: A 484 HIS cc_start: 0.6952 (m-70) cc_final: 0.6647 (m90) REVERT: B 266 MET cc_start: 0.5090 (ttm) cc_final: 0.4873 (ttp) REVERT: B 270 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.5409 (tmtt) REVERT: B 285 LYS cc_start: 0.7885 (ttmp) cc_final: 0.7224 (tttp) REVERT: B 287 SER cc_start: 0.8336 (t) cc_final: 0.7771 (p) REVERT: B 296 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7713 (tp) REVERT: C 287 SER cc_start: 0.8332 (t) cc_final: 0.7764 (p) REVERT: C 296 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7500 (tp) REVERT: C 297 MET cc_start: 0.8769 (mtp) cc_final: 0.8442 (mtp) REVERT: C 338 MET cc_start: 0.7447 (mmp) cc_final: 0.7166 (mmp) REVERT: C 413 MET cc_start: 0.5047 (tpp) cc_final: 0.4661 (mpp) REVERT: C 447 LYS cc_start: 0.6892 (tptm) cc_final: 0.5272 (tttm) REVERT: D 285 LYS cc_start: 0.7518 (ttmp) cc_final: 0.6939 (tttp) REVERT: D 287 SER cc_start: 0.8480 (t) cc_final: 0.7909 (p) REVERT: D 474 LEU cc_start: 0.5554 (OUTLIER) cc_final: 0.5110 (tt) REVERT: E 270 LYS cc_start: 0.5606 (OUTLIER) cc_final: 0.5286 (tmtt) REVERT: E 278 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6737 (tt0) REVERT: E 285 LYS cc_start: 0.7570 (ttmp) cc_final: 0.6968 (ttmt) REVERT: E 287 SER cc_start: 0.8437 (t) cc_final: 0.7829 (p) REVERT: E 339 GLN cc_start: 0.7993 (mt0) cc_final: 0.7607 (mt0) REVERT: E 460 ARG cc_start: 0.7007 (tpt170) cc_final: 0.6672 (tpt90) REVERT: F 287 SER cc_start: 0.8453 (t) cc_final: 0.7772 (p) REVERT: F 413 MET cc_start: 0.5475 (tpp) cc_final: 0.5083 (mpp) REVERT: G 270 LYS cc_start: 0.5686 (OUTLIER) cc_final: 0.5428 (tmtt) REVERT: G 285 LYS cc_start: 0.7634 (ttmp) cc_final: 0.7026 (tttp) REVERT: G 287 SER cc_start: 0.8509 (t) cc_final: 0.7908 (p) REVERT: G 436 GLU cc_start: 0.7870 (mp0) cc_final: 0.7408 (mt-10) REVERT: G 460 ARG cc_start: 0.6818 (tpt170) cc_final: 0.6435 (tpm170) outliers start: 120 outliers final: 88 residues processed: 314 average time/residue: 0.2577 time to fit residues: 119.6522 Evaluate side-chains 295 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 200 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 469 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 0.2980 chunk 130 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 170 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN C 339 GLN C 457 ASN C 484 HIS D 470 GLN D 484 HIS F 470 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15407 Z= 0.163 Angle : 0.600 7.038 20853 Z= 0.308 Chirality : 0.044 0.139 2527 Planarity : 0.003 0.030 2604 Dihedral : 5.475 16.788 2114 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.96 % Allowed : 16.30 % Favored : 76.74 % 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: -3.84 (0.17), residues: 1995 helix: -1.47 (0.17), residues: 924 sheet: -1.75 (0.32), residues: 238 loop : -4.10 (0.16), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 397 HIS 0.005 0.001 HIS D 484 PHE 0.008 0.001 PHE G 432 TYR 0.005 0.001 TYR E 441 ARG 0.002 0.000 ARG G 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 207 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6440 (tp30) cc_final: 0.5828 (mt-10) REVERT: A 287 SER cc_start: 0.8476 (t) cc_final: 0.7780 (p) REVERT: A 368 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8322 (m) REVERT: A 474 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.5061 (tt) REVERT: A 484 HIS cc_start: 0.6982 (m-70) cc_final: 0.6717 (m90) REVERT: B 266 MET cc_start: 0.4582 (ttm) cc_final: 0.4326 (ttp) REVERT: B 285 LYS cc_start: 0.7866 (ttmp) cc_final: 0.7207 (tttp) REVERT: B 287 SER cc_start: 0.8228 (t) cc_final: 0.7642 (p) REVERT: B 479 LYS cc_start: 0.5639 (mtpt) cc_final: 0.5072 (mttp) REVERT: C 287 SER cc_start: 0.8320 (t) cc_final: 0.7717 (p) REVERT: C 297 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8446 (mtp) REVERT: C 368 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8382 (m) REVERT: C 413 MET cc_start: 0.5289 (tpp) cc_final: 0.4880 (mpp) REVERT: C 447 LYS cc_start: 0.6900 (tptm) cc_final: 0.5290 (tttm) REVERT: D 278 GLU cc_start: 0.6809 (tp30) cc_final: 0.6055 (tt0) REVERT: D 287 SER cc_start: 0.8405 (t) cc_final: 0.7834 (p) REVERT: D 368 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8365 (m) REVERT: D 474 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5158 (tt) REVERT: E 270 LYS cc_start: 0.5345 (OUTLIER) cc_final: 0.5069 (tmtt) REVERT: E 278 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6707 (tt0) REVERT: E 285 LYS cc_start: 0.7509 (ttmp) cc_final: 0.6886 (ttmt) REVERT: E 287 SER cc_start: 0.8243 (t) cc_final: 0.7591 (p) REVERT: E 339 GLN cc_start: 0.8047 (mt0) cc_final: 0.7609 (mt0) REVERT: E 378 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7828 (mp) REVERT: E 479 LYS cc_start: 0.5470 (mtpt) cc_final: 0.4848 (mttm) REVERT: F 270 LYS cc_start: 0.5621 (OUTLIER) cc_final: 0.5277 (tmtt) REVERT: F 287 SER cc_start: 0.8409 (t) cc_final: 0.7747 (p) REVERT: F 457 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6759 (m-40) REVERT: G 287 SER cc_start: 0.8525 (t) cc_final: 0.7880 (p) REVERT: G 400 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6416 (pt) REVERT: G 436 GLU cc_start: 0.7857 (mp0) cc_final: 0.7423 (mt-10) REVERT: G 460 ARG cc_start: 0.6815 (tpt170) cc_final: 0.6509 (tpm170) outliers start: 114 outliers final: 80 residues processed: 295 average time/residue: 0.2567 time to fit residues: 111.7753 Evaluate side-chains 291 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 200 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 457 ASN Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 400 ILE Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.3980 chunk 170 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN B 457 ASN B 470 GLN C 339 GLN C 457 ASN C 484 HIS D 484 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15407 Z= 0.167 Angle : 0.597 7.543 20853 Z= 0.305 Chirality : 0.044 0.137 2527 Planarity : 0.003 0.026 2604 Dihedral : 5.343 16.453 2114 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.23 % Allowed : 17.58 % Favored : 76.19 % 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: -3.60 (0.17), residues: 1995 helix: -1.28 (0.17), residues: 931 sheet: -1.65 (0.33), residues: 238 loop : -3.98 (0.16), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 397 HIS 0.003 0.000 HIS C 484 PHE 0.007 0.001 PHE A 432 TYR 0.004 0.001 TYR D 467 ARG 0.005 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 194 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6392 (tp30) cc_final: 0.5821 (mt-10) REVERT: A 287 SER cc_start: 0.8460 (t) cc_final: 0.7763 (p) REVERT: A 413 MET cc_start: 0.4867 (tpp) cc_final: 0.4477 (mpp) REVERT: A 474 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.5017 (tt) REVERT: A 484 HIS cc_start: 0.6913 (m-70) cc_final: 0.6441 (m90) REVERT: B 278 GLU cc_start: 0.6924 (tp30) cc_final: 0.6277 (mt-10) REVERT: B 285 LYS cc_start: 0.7868 (ttmp) cc_final: 0.7146 (tttp) REVERT: B 287 SER cc_start: 0.8249 (t) cc_final: 0.7636 (p) REVERT: B 479 LYS cc_start: 0.5566 (mtpt) cc_final: 0.5025 (mttp) REVERT: B 484 HIS cc_start: 0.6927 (m-70) cc_final: 0.6717 (m90) REVERT: C 287 SER cc_start: 0.8408 (t) cc_final: 0.7794 (p) REVERT: C 413 MET cc_start: 0.5318 (tpp) cc_final: 0.4891 (mpp) REVERT: C 447 LYS cc_start: 0.6898 (tptm) cc_final: 0.5287 (tttm) REVERT: D 278 GLU cc_start: 0.6823 (tp30) cc_final: 0.6130 (tt0) REVERT: D 287 SER cc_start: 0.8433 (t) cc_final: 0.7866 (p) REVERT: D 446 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5924 (mm-30) REVERT: D 474 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5066 (tt) REVERT: E 270 LYS cc_start: 0.5477 (OUTLIER) cc_final: 0.5232 (tmtt) REVERT: E 278 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6834 (tt0) REVERT: E 285 LYS cc_start: 0.7451 (ttmp) cc_final: 0.6815 (ttmt) REVERT: E 287 SER cc_start: 0.8233 (t) cc_final: 0.7592 (p) REVERT: E 326 ARG cc_start: 0.7677 (ptt-90) cc_final: 0.7287 (ptt-90) REVERT: E 339 GLN cc_start: 0.8048 (mt0) cc_final: 0.7587 (mt0) REVERT: E 378 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7806 (mp) REVERT: F 270 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.5232 (tmtt) REVERT: F 287 SER cc_start: 0.8443 (t) cc_final: 0.7772 (p) REVERT: F 413 MET cc_start: 0.6028 (ptm) cc_final: 0.5274 (tpt) REVERT: F 457 ASN cc_start: 0.7235 (OUTLIER) cc_final: 0.6838 (m-40) REVERT: F 461 MET cc_start: 0.7338 (mmt) cc_final: 0.7098 (mtp) REVERT: G 285 LYS cc_start: 0.7573 (ttmp) cc_final: 0.6958 (tttp) REVERT: G 287 SER cc_start: 0.8551 (t) cc_final: 0.7913 (p) REVERT: G 436 GLU cc_start: 0.7868 (mp0) cc_final: 0.7464 (mt-10) REVERT: G 461 MET cc_start: 0.7437 (mtp) cc_final: 0.6911 (mtt) outliers start: 102 outliers final: 81 residues processed: 278 average time/residue: 0.2592 time to fit residues: 107.3207 Evaluate side-chains 273 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 185 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain F residue 483 LYS Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 ASN C 339 GLN C 484 HIS D 484 HIS E 470 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15407 Z= 0.187 Angle : 0.605 7.943 20853 Z= 0.308 Chirality : 0.044 0.137 2527 Planarity : 0.003 0.028 2604 Dihedral : 5.306 16.678 2114 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 6.23 % Allowed : 18.25 % Favored : 75.52 % 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: -3.46 (0.17), residues: 1995 helix: -1.19 (0.16), residues: 973 sheet: -2.09 (0.31), residues: 266 loop : -3.84 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 397 HIS 0.003 0.001 HIS C 484 PHE 0.007 0.001 PHE D 323 TYR 0.005 0.001 TYR D 467 ARG 0.007 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 200 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6364 (tp30) cc_final: 0.5819 (mt-10) REVERT: A 287 SER cc_start: 0.8500 (t) cc_final: 0.7796 (p) REVERT: A 400 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6510 (pt) REVERT: A 413 MET cc_start: 0.4660 (tpp) cc_final: 0.4441 (mpp) REVERT: A 424 MET cc_start: 0.7537 (tmm) cc_final: 0.7308 (ppp) REVERT: B 285 LYS cc_start: 0.7881 (ttmp) cc_final: 0.7146 (tttp) REVERT: B 287 SER cc_start: 0.8333 (t) cc_final: 0.7752 (p) REVERT: B 479 LYS cc_start: 0.5490 (mtpt) cc_final: 0.4950 (mttp) REVERT: C 285 LYS cc_start: 0.7457 (ttmp) cc_final: 0.6678 (tttp) REVERT: C 287 SER cc_start: 0.8393 (t) cc_final: 0.7788 (p) REVERT: C 413 MET cc_start: 0.5085 (tpp) cc_final: 0.4595 (mpp) REVERT: C 447 LYS cc_start: 0.6915 (tptm) cc_final: 0.5298 (tttm) REVERT: D 270 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.5647 (tmtt) REVERT: D 278 GLU cc_start: 0.6801 (tp30) cc_final: 0.6209 (tt0) REVERT: D 285 LYS cc_start: 0.7512 (ttmp) cc_final: 0.6836 (tttp) REVERT: D 287 SER cc_start: 0.8445 (t) cc_final: 0.7877 (p) REVERT: D 338 MET cc_start: 0.7541 (mmp) cc_final: 0.7072 (mmp) REVERT: D 474 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.4980 (tt) REVERT: E 278 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6857 (tt0) REVERT: E 285 LYS cc_start: 0.7459 (ttmp) cc_final: 0.6810 (ttmt) REVERT: E 287 SER cc_start: 0.8238 (t) cc_final: 0.7575 (p) REVERT: E 326 ARG cc_start: 0.7671 (ptt-90) cc_final: 0.7264 (ptt-90) REVERT: E 339 GLN cc_start: 0.8041 (mt0) cc_final: 0.7559 (mt0) REVERT: E 378 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7829 (mp) REVERT: E 479 LYS cc_start: 0.5559 (mtpt) cc_final: 0.4888 (mttm) REVERT: F 270 LYS cc_start: 0.5463 (OUTLIER) cc_final: 0.5144 (tmtt) REVERT: F 287 SER cc_start: 0.8460 (t) cc_final: 0.7798 (p) REVERT: F 413 MET cc_start: 0.6027 (ptm) cc_final: 0.5257 (tpt) REVERT: F 457 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.6914 (m-40) REVERT: G 270 LYS cc_start: 0.5790 (OUTLIER) cc_final: 0.5389 (tmtt) REVERT: G 285 LYS cc_start: 0.7569 (ttmp) cc_final: 0.6946 (tttp) REVERT: G 287 SER cc_start: 0.8566 (t) cc_final: 0.7922 (p) REVERT: G 326 ARG cc_start: 0.7387 (ptt-90) cc_final: 0.7163 (ptt-90) REVERT: G 436 GLU cc_start: 0.7885 (mp0) cc_final: 0.7437 (mt-10) outliers start: 102 outliers final: 82 residues processed: 284 average time/residue: 0.2635 time to fit residues: 110.7280 Evaluate side-chains 282 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 193 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 433 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.0770 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 148 optimal weight: 0.0970 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 ASN C 339 GLN C 484 HIS D 484 HIS F 471 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15407 Z= 0.157 Angle : 0.592 11.901 20853 Z= 0.299 Chirality : 0.044 0.133 2527 Planarity : 0.003 0.028 2604 Dihedral : 5.136 16.709 2114 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 6.11 % Allowed : 18.80 % Favored : 75.09 % 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: -3.15 (0.17), residues: 1995 helix: -0.98 (0.17), residues: 980 sheet: -1.59 (0.33), residues: 238 loop : -3.74 (0.18), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 397 HIS 0.003 0.001 HIS C 484 PHE 0.006 0.001 PHE A 432 TYR 0.005 0.001 TYR F 467 ARG 0.007 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 191 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6296 (tp30) cc_final: 0.5803 (mt-10) REVERT: A 287 SER cc_start: 0.8486 (t) cc_final: 0.7797 (p) REVERT: A 413 MET cc_start: 0.4810 (tpp) cc_final: 0.4512 (mpp) REVERT: A 424 MET cc_start: 0.7572 (tmm) cc_final: 0.7360 (ppp) REVERT: A 461 MET cc_start: 0.7507 (mtp) cc_final: 0.6944 (mtp) REVERT: B 285 LYS cc_start: 0.7863 (ttmp) cc_final: 0.7131 (tttp) REVERT: B 287 SER cc_start: 0.8327 (t) cc_final: 0.7720 (p) REVERT: B 479 LYS cc_start: 0.5634 (mtpt) cc_final: 0.5109 (mttp) REVERT: C 287 SER cc_start: 0.8397 (t) cc_final: 0.7787 (p) REVERT: C 368 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8372 (m) REVERT: C 413 MET cc_start: 0.5322 (tpp) cc_final: 0.4833 (mpp) REVERT: C 447 LYS cc_start: 0.6851 (tptm) cc_final: 0.5265 (tttm) REVERT: D 278 GLU cc_start: 0.6741 (tp30) cc_final: 0.6171 (tt0) REVERT: D 285 LYS cc_start: 0.7492 (ttmp) cc_final: 0.6843 (tttp) REVERT: D 287 SER cc_start: 0.8453 (t) cc_final: 0.7878 (p) REVERT: D 368 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8222 (m) REVERT: D 459 ILE cc_start: 0.7140 (tp) cc_final: 0.6884 (tp) REVERT: D 474 LEU cc_start: 0.5564 (OUTLIER) cc_final: 0.5017 (tt) REVERT: E 285 LYS cc_start: 0.7613 (ttmp) cc_final: 0.6845 (ttmt) REVERT: E 287 SER cc_start: 0.8204 (t) cc_final: 0.7566 (p) REVERT: E 326 ARG cc_start: 0.7601 (ptt-90) cc_final: 0.7220 (ptt-90) REVERT: E 339 GLN cc_start: 0.8013 (mt0) cc_final: 0.7502 (mt0) REVERT: E 370 LEU cc_start: 0.8482 (tp) cc_final: 0.8253 (mt) REVERT: E 378 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7817 (mp) REVERT: F 287 SER cc_start: 0.8479 (t) cc_final: 0.7815 (p) REVERT: F 338 MET cc_start: 0.7634 (mmp) cc_final: 0.7320 (mmm) REVERT: F 413 MET cc_start: 0.5962 (ptm) cc_final: 0.5240 (tpt) REVERT: F 457 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6891 (m-40) REVERT: F 466 LEU cc_start: 0.6618 (tt) cc_final: 0.6319 (tp) REVERT: G 285 LYS cc_start: 0.7497 (ttmp) cc_final: 0.6889 (tttp) REVERT: G 287 SER cc_start: 0.8391 (t) cc_final: 0.7731 (p) REVERT: G 436 GLU cc_start: 0.7910 (mp0) cc_final: 0.7450 (mt-10) outliers start: 100 outliers final: 83 residues processed: 271 average time/residue: 0.2524 time to fit residues: 102.2051 Evaluate side-chains 274 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 186 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN C 484 HIS ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15407 Z= 0.191 Angle : 0.612 11.962 20853 Z= 0.308 Chirality : 0.044 0.138 2527 Planarity : 0.003 0.031 2604 Dihedral : 5.174 16.443 2114 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 6.04 % Allowed : 19.41 % Favored : 74.54 % 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: -3.05 (0.18), residues: 1995 helix: -0.75 (0.17), residues: 945 sheet: -2.00 (0.31), residues: 266 loop : -3.66 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 397 HIS 0.003 0.001 HIS C 484 PHE 0.008 0.001 PHE D 323 TYR 0.006 0.001 TYR F 467 ARG 0.008 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 189 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6315 (tp30) cc_final: 0.5825 (mt-10) REVERT: A 287 SER cc_start: 0.8503 (t) cc_final: 0.7801 (p) REVERT: A 403 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7901 (mtpp) REVERT: A 413 MET cc_start: 0.4844 (tpp) cc_final: 0.4570 (mpp) REVERT: A 461 MET cc_start: 0.7319 (mtp) cc_final: 0.6848 (mtt) REVERT: B 285 LYS cc_start: 0.7976 (ttmp) cc_final: 0.7228 (tttp) REVERT: B 287 SER cc_start: 0.8350 (t) cc_final: 0.7740 (p) REVERT: B 459 ILE cc_start: 0.7178 (tp) cc_final: 0.6797 (tp) REVERT: B 479 LYS cc_start: 0.5581 (mtpt) cc_final: 0.5078 (mttp) REVERT: C 285 LYS cc_start: 0.7457 (ttmp) cc_final: 0.6702 (tttp) REVERT: C 287 SER cc_start: 0.8414 (t) cc_final: 0.7794 (p) REVERT: C 413 MET cc_start: 0.5123 (tpp) cc_final: 0.4621 (mpp) REVERT: C 447 LYS cc_start: 0.6862 (tptm) cc_final: 0.5263 (tttm) REVERT: D 278 GLU cc_start: 0.6731 (tp30) cc_final: 0.6171 (tt0) REVERT: D 285 LYS cc_start: 0.7501 (ttmp) cc_final: 0.6867 (tttp) REVERT: D 287 SER cc_start: 0.8431 (t) cc_final: 0.7876 (p) REVERT: D 338 MET cc_start: 0.7503 (mmp) cc_final: 0.7068 (mmp) REVERT: D 459 ILE cc_start: 0.7163 (tp) cc_final: 0.6867 (tp) REVERT: D 474 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.4937 (tt) REVERT: E 285 LYS cc_start: 0.7621 (ttmp) cc_final: 0.6947 (tttt) REVERT: E 287 SER cc_start: 0.8115 (t) cc_final: 0.7484 (p) REVERT: E 326 ARG cc_start: 0.7592 (ptt-90) cc_final: 0.7157 (ptt-90) REVERT: E 339 GLN cc_start: 0.8018 (mt0) cc_final: 0.7520 (mt0) REVERT: E 346 MET cc_start: 0.5712 (tpt) cc_final: 0.5330 (tpt) REVERT: E 378 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7820 (mp) REVERT: E 479 LYS cc_start: 0.5495 (mtpt) cc_final: 0.4860 (mttm) REVERT: F 287 SER cc_start: 0.8510 (t) cc_final: 0.7845 (p) REVERT: F 413 MET cc_start: 0.5979 (ptm) cc_final: 0.5320 (tpt) REVERT: F 457 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.7017 (m-40) REVERT: G 270 LYS cc_start: 0.5748 (OUTLIER) cc_final: 0.5270 (tmtt) REVERT: G 285 LYS cc_start: 0.7620 (ttmp) cc_final: 0.6963 (tttp) REVERT: G 287 SER cc_start: 0.8406 (t) cc_final: 0.7753 (p) REVERT: G 436 GLU cc_start: 0.7936 (mp0) cc_final: 0.7638 (mt-10) outliers start: 99 outliers final: 89 residues processed: 272 average time/residue: 0.2455 time to fit residues: 100.1531 Evaluate side-chains 276 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 183 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.0470 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN C 484 HIS D 484 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15407 Z= 0.173 Angle : 0.609 12.089 20853 Z= 0.304 Chirality : 0.044 0.136 2527 Planarity : 0.003 0.035 2604 Dihedral : 5.092 16.536 2114 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.80 % Allowed : 19.72 % Favored : 74.48 % 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: -2.90 (0.18), residues: 1995 helix: -0.64 (0.17), residues: 945 sheet: -1.57 (0.33), residues: 238 loop : -3.66 (0.17), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 397 HIS 0.003 0.001 HIS C 484 PHE 0.006 0.001 PHE D 323 TYR 0.005 0.001 TYR F 467 ARG 0.008 0.000 ARG D 426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 184 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6294 (tp30) cc_final: 0.5826 (mt-10) REVERT: A 287 SER cc_start: 0.8493 (t) cc_final: 0.7797 (p) REVERT: A 403 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7895 (mtpp) REVERT: A 413 MET cc_start: 0.4891 (tpp) cc_final: 0.4554 (mpp) REVERT: A 461 MET cc_start: 0.7366 (mtp) cc_final: 0.6832 (mtp) REVERT: A 479 LYS cc_start: 0.5563 (mtpt) cc_final: 0.4939 (mttm) REVERT: B 285 LYS cc_start: 0.7923 (ttmp) cc_final: 0.7184 (tttp) REVERT: B 287 SER cc_start: 0.8341 (t) cc_final: 0.7729 (p) REVERT: B 459 ILE cc_start: 0.7169 (tp) cc_final: 0.6750 (tp) REVERT: B 479 LYS cc_start: 0.5593 (mtpt) cc_final: 0.5094 (mttp) REVERT: C 285 LYS cc_start: 0.7407 (ttmp) cc_final: 0.6669 (tttp) REVERT: C 287 SER cc_start: 0.8412 (t) cc_final: 0.7797 (p) REVERT: C 368 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8349 (m) REVERT: C 413 MET cc_start: 0.5117 (tpp) cc_final: 0.4608 (mpp) REVERT: C 447 LYS cc_start: 0.6846 (tptm) cc_final: 0.5272 (tttm) REVERT: D 278 GLU cc_start: 0.6773 (tp30) cc_final: 0.6168 (tt0) REVERT: D 285 LYS cc_start: 0.7468 (ttmp) cc_final: 0.6832 (tttp) REVERT: D 287 SER cc_start: 0.8427 (t) cc_final: 0.7877 (p) REVERT: D 338 MET cc_start: 0.7475 (mmp) cc_final: 0.6996 (mmp) REVERT: D 413 MET cc_start: 0.5438 (ptp) cc_final: 0.4914 (tpt) REVERT: D 459 ILE cc_start: 0.7140 (tp) cc_final: 0.6840 (tp) REVERT: D 474 LEU cc_start: 0.5443 (OUTLIER) cc_final: 0.4900 (tt) REVERT: E 285 LYS cc_start: 0.7602 (ttmp) cc_final: 0.6928 (tttt) REVERT: E 287 SER cc_start: 0.8109 (t) cc_final: 0.7471 (p) REVERT: E 326 ARG cc_start: 0.7577 (ptt-90) cc_final: 0.7185 (ptt-90) REVERT: E 339 GLN cc_start: 0.7984 (mt0) cc_final: 0.7453 (mt0) REVERT: E 346 MET cc_start: 0.5757 (tpt) cc_final: 0.5384 (tpt) REVERT: E 378 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7852 (mp) REVERT: E 479 LYS cc_start: 0.5503 (mtpt) cc_final: 0.4879 (mttm) REVERT: F 287 SER cc_start: 0.8507 (t) cc_final: 0.7844 (p) REVERT: F 297 MET cc_start: 0.8544 (ttp) cc_final: 0.8295 (mtm) REVERT: F 413 MET cc_start: 0.5945 (ptm) cc_final: 0.5268 (tpt) REVERT: F 457 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6858 (m-40) REVERT: G 285 LYS cc_start: 0.7581 (ttmp) cc_final: 0.6929 (tttp) REVERT: G 287 SER cc_start: 0.8402 (t) cc_final: 0.7749 (p) REVERT: G 436 GLU cc_start: 0.7923 (mp0) cc_final: 0.7638 (mt-10) REVERT: G 461 MET cc_start: 0.7332 (mtp) cc_final: 0.6736 (mtt) outliers start: 95 outliers final: 84 residues processed: 263 average time/residue: 0.2520 time to fit residues: 99.6425 Evaluate side-chains 268 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 180 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 457 ASN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 457 ASN Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 453 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 155 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN C 484 HIS D 484 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.209543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163239 restraints weight = 14080.194| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.50 r_work: 0.3497 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15407 Z= 0.175 Angle : 0.613 12.493 20853 Z= 0.305 Chirality : 0.044 0.135 2527 Planarity : 0.003 0.035 2604 Dihedral : 5.042 16.178 2114 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.56 % Allowed : 19.84 % Favored : 74.60 % 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: -2.81 (0.18), residues: 1995 helix: -0.67 (0.17), residues: 987 sheet: -1.54 (0.34), residues: 238 loop : -3.59 (0.18), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 397 HIS 0.003 0.001 HIS C 484 PHE 0.007 0.001 PHE D 323 TYR 0.005 0.001 TYR F 467 ARG 0.008 0.000 ARG D 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3134.66 seconds wall clock time: 57 minutes 16.93 seconds (3436.93 seconds total)