Starting phenix.real_space_refine on Fri Feb 16 17:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0f_20996/02_2024/6v0f_20996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0f_20996/02_2024/6v0f_20996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0f_20996/02_2024/6v0f_20996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0f_20996/02_2024/6v0f_20996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0f_20996/02_2024/6v0f_20996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0f_20996/02_2024/6v0f_20996.pdb" } resolution = 2.96 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= 0.009 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 24 5.16 5 C 10128 2.51 5 N 2688 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 220": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 456": "NH1" <-> "NH2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 220": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 456": "NH1" <-> "NH2" Residue "F PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15942 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2657 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Chain: "B" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2657 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Chain: "C" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2657 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Chain: "D" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2657 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Chain: "E" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2657 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Chain: "F" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2657 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Time building chain proxies: 8.75, per 1000 atoms: 0.55 Number of scatterers: 15942 At special positions: 0 Unit cell: (113.97, 103.49, 119.21, 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 24 16.00 O 3102 8.00 N 2688 7.00 C 10128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 3.3 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3804 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 30 sheets defined 17.1% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.701A pdb=" N THR A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.730A pdb=" N THR A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.332A pdb=" N LEU A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.702A pdb=" N THR B 212 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.731A pdb=" N THR B 333 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.702A pdb=" N THR C 212 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.737A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.730A pdb=" N THR C 333 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU C 386 " --> pdb=" O GLY C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'D' and resid 209 through 214 removed outlier: 3.702A pdb=" N THR D 212 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.730A pdb=" N THR D 333 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU D 386 " --> pdb=" O GLY D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'E' and resid 209 through 214 removed outlier: 3.701A pdb=" N THR E 212 " --> pdb=" O ARG E 209 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP E 213 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.731A pdb=" N THR E 333 " --> pdb=" O SER E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU E 386 " --> pdb=" O GLY E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'F' and resid 209 through 214 removed outlier: 3.701A pdb=" N THR F 212 " --> pdb=" O ARG F 209 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP F 213 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 removed outlier: 4.085A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.736A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 removed outlier: 3.731A pdb=" N THR F 333 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 381 through 386 removed outlier: 4.333A pdb=" N LEU F 386 " --> pdb=" O GLY F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 500 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL A 202 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 192 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP A 204 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 3.850A pdb=" N VAL A 227 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.842A pdb=" N VAL F 227 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.115A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE A 481 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL A 421 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA A 436 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 495 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 459 through 460 removed outlier: 3.895A pdb=" N GLU A 467 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL B 202 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR B 192 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP B 204 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 230 removed outlier: 3.831A pdb=" N VAL B 227 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.114A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE B 481 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL B 421 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA B 436 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 495 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 459 through 460 removed outlier: 3.894A pdb=" N GLU B 467 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR C 192 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP C 204 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 227 through 230 removed outlier: 3.861A pdb=" N VAL C 227 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.115A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE C 481 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL C 421 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA C 436 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 495 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 459 through 460 removed outlier: 3.894A pdb=" N GLU C 467 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL D 202 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR D 192 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP D 204 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 227 through 230 removed outlier: 3.848A pdb=" N VAL D 227 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.115A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE D 481 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL D 421 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA D 436 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR D 495 " --> pdb=" O THR D 396 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 459 through 460 removed outlier: 3.895A pdb=" N GLU D 467 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL E 202 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR E 192 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP E 204 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 227 through 230 removed outlier: 3.835A pdb=" N VAL E 227 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.115A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE E 481 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL E 421 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA E 436 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E 495 " --> pdb=" O THR E 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 459 through 460 removed outlier: 3.894A pdb=" N GLU E 467 " --> pdb=" O LYS E 460 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 161 through 167 removed outlier: 7.018A pdb=" N VAL F 202 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR F 192 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP F 204 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.116A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 449 through 453 removed outlier: 3.592A pdb=" N ILE F 481 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL F 421 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA F 436 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 495 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 459 through 460 removed outlier: 3.895A pdb=" N GLU F 467 " --> pdb=" O LYS F 460 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4263 1.33 - 1.44: 2353 1.44 - 1.56: 9542 1.56 - 1.68: 6 1.68 - 1.79: 48 Bond restraints: 16212 Sorted by residual: bond pdb=" CB VAL B 307 " pdb=" CG1 VAL B 307 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.75e+00 bond pdb=" CB VAL C 307 " pdb=" CG1 VAL C 307 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.70e+00 bond pdb=" CB VAL D 307 " pdb=" CG1 VAL D 307 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.68e+00 bond pdb=" CB VAL A 307 " pdb=" CG1 VAL A 307 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.68e+00 bond pdb=" CB VAL F 307 " pdb=" CG1 VAL F 307 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.64e+00 ... (remaining 16207 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.31: 531 106.31 - 113.79: 9219 113.79 - 121.26: 7616 121.26 - 128.74: 4552 128.74 - 136.21: 78 Bond angle restraints: 21996 Sorted by residual: angle pdb=" N LEU C 444 " pdb=" CA LEU C 444 " pdb=" C LEU C 444 " ideal model delta sigma weight residual 111.33 119.87 -8.54 1.21e+00 6.83e-01 4.98e+01 angle pdb=" N LEU E 444 " pdb=" CA LEU E 444 " pdb=" C LEU E 444 " ideal model delta sigma weight residual 111.33 119.86 -8.53 1.21e+00 6.83e-01 4.98e+01 angle pdb=" N LEU A 444 " pdb=" CA LEU A 444 " pdb=" C LEU A 444 " ideal model delta sigma weight residual 111.33 119.84 -8.51 1.21e+00 6.83e-01 4.94e+01 angle pdb=" N LEU F 444 " pdb=" CA LEU F 444 " pdb=" C LEU F 444 " ideal model delta sigma weight residual 111.33 119.84 -8.51 1.21e+00 6.83e-01 4.94e+01 angle pdb=" N LEU D 444 " pdb=" CA LEU D 444 " pdb=" C LEU D 444 " ideal model delta sigma weight residual 111.33 119.82 -8.49 1.21e+00 6.83e-01 4.92e+01 ... (remaining 21991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 9339 15.79 - 31.58: 401 31.58 - 47.37: 82 47.37 - 63.16: 6 63.16 - 78.95: 24 Dihedral angle restraints: 9852 sinusoidal: 3900 harmonic: 5952 Sorted by residual: dihedral pdb=" CA LEU F 411 " pdb=" C LEU F 411 " pdb=" N ILE F 412 " pdb=" CA ILE F 412 " ideal model delta harmonic sigma weight residual -180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA LEU E 411 " pdb=" C LEU E 411 " pdb=" N ILE E 412 " pdb=" CA ILE E 412 " ideal model delta harmonic sigma weight residual 180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LEU A 411 " pdb=" C LEU A 411 " pdb=" N ILE A 412 " pdb=" CA ILE A 412 " ideal model delta harmonic sigma weight residual -180.00 -153.36 -26.64 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1594 0.059 - 0.118: 723 0.118 - 0.177: 195 0.177 - 0.236: 40 0.236 - 0.294: 34 Chirality restraints: 2586 Sorted by residual: chirality pdb=" CA ASN A 338 " pdb=" N ASN A 338 " pdb=" C ASN A 338 " pdb=" CB ASN A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASN B 338 " pdb=" N ASN B 338 " pdb=" C ASN B 338 " pdb=" CB ASN B 338 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ASN C 338 " pdb=" N ASN C 338 " pdb=" C ASN C 338 " pdb=" CB ASN C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 2583 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 491 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C MET C 491 " -0.064 2.00e-02 2.50e+03 pdb=" O MET C 491 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS C 492 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 491 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C MET F 491 " 0.064 2.00e-02 2.50e+03 pdb=" O MET F 491 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS F 492 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 491 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C MET E 491 " -0.064 2.00e-02 2.50e+03 pdb=" O MET E 491 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS E 492 " 0.021 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 6270 2.93 - 3.42: 14154 3.42 - 3.91: 25028 3.91 - 4.41: 27013 4.41 - 4.90: 47875 Nonbonded interactions: 120340 Sorted by model distance: nonbonded pdb=" NH1 ARG D 220 " pdb=" OH TYR D 271 " model vdw 2.433 2.520 nonbonded pdb=" NH1 ARG C 220 " pdb=" OH TYR C 271 " model vdw 2.433 2.520 nonbonded pdb=" NH1 ARG E 220 " pdb=" OH TYR E 271 " model vdw 2.433 2.520 nonbonded pdb=" NH1 ARG F 220 " pdb=" OH TYR F 271 " model vdw 2.433 2.520 nonbonded pdb=" NH1 ARG A 220 " pdb=" OH TYR A 271 " model vdw 2.433 2.520 ... (remaining 120335 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' } 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: 1.160 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: 5.400 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 44.640 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 16212 Z= 0.638 Angle : 1.332 19.912 21996 Z= 0.712 Chirality : 0.074 0.294 2586 Planarity : 0.009 0.061 2856 Dihedral : 10.493 78.952 6048 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.34 % Allowed : 3.70 % Favored : 95.96 % 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: -2.57 (0.15), residues: 2094 helix: -2.11 (0.28), residues: 234 sheet: -1.13 (0.19), residues: 666 loop : -1.99 (0.14), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 222 HIS 0.020 0.006 HIS C 441 PHE 0.036 0.004 PHE C 221 TYR 0.011 0.002 TYR F 403 ARG 0.005 0.001 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 455 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8671 (mtt-85) cc_final: 0.8318 (mtp180) REVERT: A 248 ASN cc_start: 0.6725 (t0) cc_final: 0.6513 (p0) REVERT: A 278 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8063 (mp10) REVERT: A 456 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6706 (mmm160) REVERT: B 278 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8080 (mp10) REVERT: B 312 LYS cc_start: 0.8195 (tttt) cc_final: 0.7986 (tttp) REVERT: B 314 ASP cc_start: 0.7171 (m-30) cc_final: 0.6929 (m-30) REVERT: B 425 LYS cc_start: 0.8026 (tttm) cc_final: 0.7809 (mttm) REVERT: C 220 ARG cc_start: 0.8764 (mtt-85) cc_final: 0.8545 (mtp180) REVERT: C 273 ASP cc_start: 0.7799 (t0) cc_final: 0.7553 (t0) REVERT: C 297 SER cc_start: 0.8480 (m) cc_final: 0.8219 (t) REVERT: C 312 LYS cc_start: 0.8293 (tttt) cc_final: 0.8088 (tttm) REVERT: C 425 LYS cc_start: 0.8011 (tttm) cc_final: 0.7745 (mttm) REVERT: D 246 LEU cc_start: 0.8359 (mp) cc_final: 0.8039 (tm) REVERT: D 278 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8065 (mp10) REVERT: D 456 ARG cc_start: 0.7558 (mtm110) cc_final: 0.6650 (mmm160) REVERT: E 314 ASP cc_start: 0.7194 (m-30) cc_final: 0.6946 (m-30) REVERT: F 297 SER cc_start: 0.8458 (m) cc_final: 0.8213 (t) outliers start: 6 outliers final: 6 residues processed: 461 average time/residue: 1.4216 time to fit residues: 715.0716 Evaluate side-chains 244 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 238 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 354 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 0.0170 chunk 85 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 345 ASN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS B 174 ASN B 345 ASN B 417 GLN B 440 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 440 GLN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 345 ASN D 417 GLN D 440 GLN ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 174 ASN E 345 ASN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN E 440 GLN ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 440 GLN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16212 Z= 0.248 Angle : 0.715 10.921 21996 Z= 0.354 Chirality : 0.049 0.154 2586 Planarity : 0.005 0.049 2856 Dihedral : 5.607 36.484 2238 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.66 % Allowed : 17.69 % Favored : 77.65 % 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: -1.92 (0.16), residues: 2094 helix: -2.35 (0.21), residues: 258 sheet: -0.30 (0.20), residues: 684 loop : -1.63 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 222 HIS 0.004 0.001 HIS D 441 PHE 0.013 0.002 PHE C 364 TYR 0.013 0.001 TYR C 192 ARG 0.006 0.001 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 254 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.6831 (t0) cc_final: 0.6592 (p0) REVERT: A 302 TYR cc_start: 0.8996 (t80) cc_final: 0.8778 (t80) REVERT: A 409 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: A 456 ARG cc_start: 0.7600 (mtm110) cc_final: 0.6837 (mmm160) REVERT: A 482 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7287 (ttt90) REVERT: A 505 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8866 (mm) REVERT: B 278 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8066 (mp10) REVERT: B 482 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7636 (ttt90) REVERT: C 278 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: C 297 SER cc_start: 0.8575 (m) cc_final: 0.8342 (t) REVERT: C 312 LYS cc_start: 0.8218 (tttt) cc_final: 0.7903 (ttpt) REVERT: D 302 TYR cc_start: 0.8971 (t80) cc_final: 0.8751 (t80) REVERT: D 312 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7688 (ttpt) REVERT: D 456 ARG cc_start: 0.7549 (mtm110) cc_final: 0.6776 (mmm160) REVERT: E 370 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7741 (p0) REVERT: E 409 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8348 (mt0) REVERT: E 456 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7253 (mtt180) REVERT: E 482 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7583 (ttt90) REVERT: F 278 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: F 297 SER cc_start: 0.8502 (m) cc_final: 0.8254 (t) outliers start: 82 outliers final: 26 residues processed: 308 average time/residue: 1.3013 time to fit residues: 441.5536 Evaluate side-chains 250 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 508 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 189 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 309 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 417 GLN C 316 ASN C 420 GLN D 316 ASN E 316 ASN E 417 GLN F 316 ASN F 420 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16212 Z= 0.387 Angle : 0.732 10.029 21996 Z= 0.371 Chirality : 0.052 0.164 2586 Planarity : 0.005 0.049 2856 Dihedral : 5.610 28.885 2230 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 6.20 % Allowed : 17.92 % Favored : 75.88 % 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: -1.78 (0.17), residues: 2094 helix: -3.22 (0.20), residues: 258 sheet: -0.09 (0.20), residues: 666 loop : -1.34 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 222 HIS 0.004 0.001 HIS A 441 PHE 0.020 0.002 PHE F 364 TYR 0.008 0.001 TYR D 302 ARG 0.004 0.001 ARG F 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 227 time to evaluate : 1.955 Fit side-chains REVERT: A 209 ARG cc_start: 0.5810 (OUTLIER) cc_final: 0.4687 (ttt90) REVERT: A 278 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7090 (mp10) REVERT: A 409 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8412 (mt0) REVERT: A 456 ARG cc_start: 0.7660 (mtm110) cc_final: 0.6898 (mmm160) REVERT: A 482 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7489 (ttt90) REVERT: B 278 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8064 (mp10) REVERT: B 312 LYS cc_start: 0.8064 (tttt) cc_final: 0.7793 (ttpt) REVERT: B 456 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7272 (mtt180) REVERT: B 482 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7830 (ttt90) REVERT: C 278 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: C 386 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8309 (tp) REVERT: D 208 GLU cc_start: 0.7650 (tp30) cc_final: 0.7398 (mm-30) REVERT: D 278 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7074 (mp10) REVERT: D 312 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7754 (ttpt) REVERT: D 393 LEU cc_start: 0.8601 (tt) cc_final: 0.8353 (tm) REVERT: D 456 ARG cc_start: 0.7485 (mtm110) cc_final: 0.6765 (mmm160) REVERT: E 370 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7595 (p0) REVERT: E 456 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7309 (mtt180) REVERT: E 482 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7898 (ttt90) REVERT: F 209 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.4637 (ttt90) REVERT: F 271 TYR cc_start: 0.8460 (m-80) cc_final: 0.8229 (m-10) REVERT: F 278 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: F 297 SER cc_start: 0.8656 (m) cc_final: 0.8456 (t) REVERT: F 386 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8268 (tp) outliers start: 109 outliers final: 49 residues processed: 300 average time/residue: 1.2452 time to fit residues: 413.2044 Evaluate side-chains 259 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 196 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 508 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 202 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16212 Z= 0.246 Angle : 0.639 8.687 21996 Z= 0.324 Chirality : 0.048 0.153 2586 Planarity : 0.004 0.046 2856 Dihedral : 5.153 22.475 2226 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 6.60 % Allowed : 18.77 % Favored : 74.63 % 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: -1.63 (0.17), residues: 2094 helix: -3.01 (0.22), residues: 258 sheet: 0.03 (0.20), residues: 684 loop : -1.31 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 222 HIS 0.003 0.001 HIS A 441 PHE 0.011 0.001 PHE F 364 TYR 0.011 0.001 TYR D 302 ARG 0.003 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 212 time to evaluate : 1.854 Fit side-chains REVERT: A 208 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: A 209 ARG cc_start: 0.5887 (OUTLIER) cc_final: 0.4801 (ttt90) REVERT: A 278 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: A 302 TYR cc_start: 0.8940 (t80) cc_final: 0.8689 (t80) REVERT: A 456 ARG cc_start: 0.7537 (mtm110) cc_final: 0.6904 (mmm160) REVERT: A 482 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7390 (ttt90) REVERT: A 491 MET cc_start: 0.8574 (mmm) cc_final: 0.8348 (tpt) REVERT: A 501 LEU cc_start: 0.8939 (tp) cc_final: 0.8635 (tm) REVERT: B 278 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8058 (mp10) REVERT: B 309 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7451 (tp-100) REVERT: B 395 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7732 (mt) REVERT: B 456 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7268 (mtt180) REVERT: B 482 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7816 (ttt90) REVERT: C 206 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8912 (tp) REVERT: C 278 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: D 208 GLU cc_start: 0.7663 (tp30) cc_final: 0.7434 (mm-30) REVERT: D 278 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: D 302 TYR cc_start: 0.8962 (t80) cc_final: 0.8707 (t80) REVERT: D 312 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7859 (ttpt) REVERT: D 456 ARG cc_start: 0.7451 (mtm110) cc_final: 0.6794 (mmm160) REVERT: D 501 LEU cc_start: 0.8851 (tp) cc_final: 0.8390 (tm) REVERT: E 278 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: E 309 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7492 (tp-100) REVERT: E 370 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7579 (p0) REVERT: E 456 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7256 (mtt180) REVERT: E 482 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7755 (ttt90) REVERT: F 278 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7769 (mp10) outliers start: 116 outliers final: 50 residues processed: 294 average time/residue: 1.2404 time to fit residues: 404.1775 Evaluate side-chains 253 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 187 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 508 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.3980 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 420 GLN F 440 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16212 Z= 0.233 Angle : 0.633 8.975 21996 Z= 0.318 Chirality : 0.047 0.149 2586 Planarity : 0.004 0.044 2856 Dihedral : 4.950 21.930 2226 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 6.88 % Allowed : 18.71 % Favored : 74.40 % 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: -1.46 (0.17), residues: 2094 helix: -2.82 (0.24), residues: 258 sheet: 0.31 (0.20), residues: 672 loop : -1.31 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 222 HIS 0.003 0.001 HIS A 441 PHE 0.009 0.001 PHE F 364 TYR 0.010 0.001 TYR D 302 ARG 0.002 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 204 time to evaluate : 1.881 Fit side-chains REVERT: A 206 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 209 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.4876 (ttt90) REVERT: A 278 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: A 302 TYR cc_start: 0.8920 (t80) cc_final: 0.8692 (t80) REVERT: A 456 ARG cc_start: 0.7507 (mtm110) cc_final: 0.6905 (mmm160) REVERT: A 482 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7344 (ttt90) REVERT: A 501 LEU cc_start: 0.8973 (tp) cc_final: 0.8754 (tm) REVERT: B 278 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8135 (mp10) REVERT: B 309 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7456 (tp-100) REVERT: B 456 ARG cc_start: 0.7471 (mtt180) cc_final: 0.7222 (mtt180) REVERT: B 482 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7861 (ttt90) REVERT: C 206 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8909 (tp) REVERT: C 209 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.4381 (ttt90) REVERT: C 278 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: D 206 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8706 (mp) REVERT: D 278 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7055 (mp10) REVERT: D 312 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7881 (ttpt) REVERT: D 456 ARG cc_start: 0.7451 (mtm110) cc_final: 0.6847 (mmm160) REVERT: E 278 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: E 370 ASP cc_start: 0.7813 (p0) cc_final: 0.7477 (p0) REVERT: E 456 ARG cc_start: 0.7458 (mtt180) cc_final: 0.6755 (mmt180) REVERT: E 482 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7831 (ttt90) REVERT: F 278 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7740 (mp10) outliers start: 121 outliers final: 55 residues processed: 297 average time/residue: 1.1678 time to fit residues: 385.5023 Evaluate side-chains 259 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 189 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 203 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN B 417 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN D 309 GLN E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16212 Z= 0.351 Angle : 0.698 9.878 21996 Z= 0.348 Chirality : 0.050 0.156 2586 Planarity : 0.005 0.048 2856 Dihedral : 5.167 23.097 2226 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 7.91 % Allowed : 18.32 % Favored : 73.78 % 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: -1.51 (0.17), residues: 2094 helix: -2.87 (0.24), residues: 258 sheet: 0.40 (0.21), residues: 576 loop : -1.30 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 222 HIS 0.003 0.001 HIS B 441 PHE 0.013 0.002 PHE E 364 TYR 0.011 0.001 TYR D 302 ARG 0.002 0.000 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 200 time to evaluate : 1.848 Fit side-chains REVERT: A 209 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.4592 (ttt90) REVERT: A 278 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: A 456 ARG cc_start: 0.7573 (mtm110) cc_final: 0.6848 (mmm160) REVERT: A 482 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7402 (ttt90) REVERT: B 278 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8155 (mp10) REVERT: B 309 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7482 (tp-100) REVERT: B 402 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8886 (p) REVERT: B 409 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8438 (mt0) REVERT: B 456 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6365 (mmt180) REVERT: B 482 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7996 (ttt90) REVERT: C 206 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8948 (tp) REVERT: C 209 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.4479 (ttt90) REVERT: C 278 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: C 395 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8012 (mt) REVERT: D 206 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8735 (mp) REVERT: D 209 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.4585 (ttt90) REVERT: D 271 TYR cc_start: 0.8391 (m-80) cc_final: 0.8148 (m-10) REVERT: D 278 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: D 302 TYR cc_start: 0.8957 (t80) cc_final: 0.8626 (t80) REVERT: D 312 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7846 (ttpt) REVERT: D 456 ARG cc_start: 0.7452 (mtm110) cc_final: 0.6795 (mmm160) REVERT: E 278 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: E 370 ASP cc_start: 0.7862 (p0) cc_final: 0.7506 (p0) REVERT: E 402 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8890 (p) REVERT: E 409 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8684 (mt0) REVERT: E 456 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7274 (mtt180) REVERT: F 278 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7703 (mp10) outliers start: 139 outliers final: 69 residues processed: 300 average time/residue: 1.1331 time to fit residues: 379.4979 Evaluate side-chains 278 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 192 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 425 LYS Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 508 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 126 optimal weight: 0.4980 chunk 123 optimal weight: 0.9990 chunk 93 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN C 440 GLN D 440 GLN E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16212 Z= 0.207 Angle : 0.641 8.749 21996 Z= 0.317 Chirality : 0.047 0.145 2586 Planarity : 0.004 0.046 2856 Dihedral : 4.806 22.072 2226 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.37 % Allowed : 20.19 % Favored : 73.44 % 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: -1.39 (0.17), residues: 2094 helix: -2.71 (0.25), residues: 258 sheet: 0.50 (0.21), residues: 576 loop : -1.24 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 222 HIS 0.004 0.001 HIS D 441 PHE 0.010 0.001 PHE F 253 TYR 0.006 0.001 TYR D 302 ARG 0.003 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 213 time to evaluate : 1.917 Fit side-chains REVERT: A 209 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.4634 (ttt90) REVERT: A 456 ARG cc_start: 0.7503 (mtm110) cc_final: 0.6887 (mmm160) REVERT: A 482 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7356 (ttt90) REVERT: A 501 LEU cc_start: 0.8841 (tp) cc_final: 0.8620 (tm) REVERT: B 278 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8089 (mp10) REVERT: B 309 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7414 (tp-100) REVERT: B 402 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8860 (p) REVERT: B 409 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8222 (mt0) REVERT: B 456 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6367 (mmt180) REVERT: B 482 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7710 (ttt90) REVERT: C 206 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8884 (tp) REVERT: C 209 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.4538 (ttt90) REVERT: C 233 ILE cc_start: 0.5300 (OUTLIER) cc_final: 0.4803 (mp) REVERT: C 278 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7874 (mp10) REVERT: C 395 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7959 (mt) REVERT: D 209 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.4605 (ttt90) REVERT: D 278 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7042 (mp10) REVERT: D 302 TYR cc_start: 0.8904 (t80) cc_final: 0.8553 (t80) REVERT: D 456 ARG cc_start: 0.7405 (mtm110) cc_final: 0.6791 (mmm160) REVERT: E 278 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: E 370 ASP cc_start: 0.7818 (p0) cc_final: 0.7456 (p0) REVERT: E 402 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8846 (p) REVERT: E 456 ARG cc_start: 0.7334 (mtt180) cc_final: 0.7112 (mtt180) REVERT: F 233 ILE cc_start: 0.5265 (OUTLIER) cc_final: 0.4734 (mp) REVERT: F 278 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: F 363 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8356 (p) outliers start: 112 outliers final: 57 residues processed: 297 average time/residue: 1.1579 time to fit residues: 382.6250 Evaluate side-chains 268 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 194 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 159 optimal weight: 0.0970 chunk 184 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16212 Z= 0.213 Angle : 0.655 9.810 21996 Z= 0.322 Chirality : 0.047 0.146 2586 Planarity : 0.004 0.046 2856 Dihedral : 4.736 21.782 2226 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 6.26 % Allowed : 21.10 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.17), residues: 2094 helix: -2.69 (0.25), residues: 258 sheet: 0.57 (0.21), residues: 576 loop : -1.17 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 222 HIS 0.004 0.001 HIS D 441 PHE 0.012 0.001 PHE E 451 TYR 0.020 0.001 TYR A 302 ARG 0.002 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 205 time to evaluate : 1.930 Fit side-chains REVERT: A 209 ARG cc_start: 0.5763 (OUTLIER) cc_final: 0.4676 (ttt90) REVERT: A 302 TYR cc_start: 0.8801 (t80) cc_final: 0.8427 (t80) REVERT: A 456 ARG cc_start: 0.7477 (mtm110) cc_final: 0.6860 (mmm160) REVERT: A 482 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7387 (ttt90) REVERT: B 278 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8086 (mp10) REVERT: B 409 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8420 (mt0) REVERT: B 411 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7691 (tt) REVERT: B 482 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7893 (ttt90) REVERT: C 233 ILE cc_start: 0.5299 (OUTLIER) cc_final: 0.4808 (mp) REVERT: C 278 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: D 209 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.4666 (ttt90) REVERT: D 278 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7062 (mp10) REVERT: D 302 TYR cc_start: 0.8881 (t80) cc_final: 0.8505 (t80) REVERT: D 312 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7882 (ttpt) REVERT: D 456 ARG cc_start: 0.7459 (mtm110) cc_final: 0.6841 (mmm160) REVERT: E 278 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: E 370 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7446 (p0) REVERT: E 402 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8857 (p) REVERT: E 409 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8480 (mt0) REVERT: E 411 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7819 (tt) REVERT: F 233 ILE cc_start: 0.5270 (OUTLIER) cc_final: 0.4748 (mp) REVERT: F 278 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: F 491 MET cc_start: 0.8420 (mmm) cc_final: 0.8187 (mmm) outliers start: 110 outliers final: 65 residues processed: 287 average time/residue: 1.1540 time to fit residues: 369.7403 Evaluate side-chains 276 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 196 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 170 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 123 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 GLN B 440 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16212 Z= 0.223 Angle : 0.664 9.537 21996 Z= 0.327 Chirality : 0.047 0.145 2586 Planarity : 0.004 0.045 2856 Dihedral : 4.695 21.930 2226 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.57 % Allowed : 21.84 % Favored : 72.58 % 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: -1.25 (0.17), residues: 2094 helix: -2.62 (0.25), residues: 258 sheet: 0.60 (0.21), residues: 576 loop : -1.15 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 222 HIS 0.004 0.001 HIS D 441 PHE 0.010 0.001 PHE E 451 TYR 0.019 0.001 TYR A 302 ARG 0.002 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 207 time to evaluate : 2.014 Fit side-chains REVERT: A 209 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.4816 (ttt90) REVERT: A 456 ARG cc_start: 0.7492 (mtm110) cc_final: 0.6865 (mmm160) REVERT: A 482 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7385 (ttt90) REVERT: B 278 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8078 (mp10) REVERT: B 402 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8886 (p) REVERT: B 409 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8454 (mt0) REVERT: B 411 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7703 (tt) REVERT: B 482 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7727 (ttt90) REVERT: C 233 ILE cc_start: 0.5286 (OUTLIER) cc_final: 0.4797 (mp) REVERT: C 278 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: C 456 ARG cc_start: 0.7112 (mtt-85) cc_final: 0.6536 (mmm160) REVERT: D 209 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.4681 (ttt90) REVERT: D 278 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: D 302 TYR cc_start: 0.8870 (t80) cc_final: 0.8544 (t80) REVERT: D 312 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7898 (ttpt) REVERT: D 456 ARG cc_start: 0.7477 (mtm110) cc_final: 0.6841 (mmm160) REVERT: E 278 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: E 370 ASP cc_start: 0.7808 (p0) cc_final: 0.7443 (p0) REVERT: E 402 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8857 (p) REVERT: E 409 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8439 (mt0) REVERT: E 411 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7806 (tt) REVERT: F 162 MET cc_start: 0.7709 (ttp) cc_final: 0.7322 (ttm) REVERT: F 233 ILE cc_start: 0.5269 (OUTLIER) cc_final: 0.4745 (mp) REVERT: F 278 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: F 491 MET cc_start: 0.8344 (mmm) cc_final: 0.7958 (tpt) outliers start: 98 outliers final: 66 residues processed: 277 average time/residue: 1.1453 time to fit residues: 355.0845 Evaluate side-chains 281 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 200 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 508 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 128 optimal weight: 0.0570 chunk 102 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16212 Z= 0.226 Angle : 0.670 9.341 21996 Z= 0.331 Chirality : 0.047 0.145 2586 Planarity : 0.004 0.046 2856 Dihedral : 4.707 21.854 2226 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.35 % Allowed : 22.47 % Favored : 72.18 % 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: -1.22 (0.17), residues: 2094 helix: -2.60 (0.26), residues: 258 sheet: 0.61 (0.22), residues: 576 loop : -1.12 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 222 HIS 0.004 0.001 HIS D 441 PHE 0.010 0.001 PHE E 451 TYR 0.008 0.001 TYR A 302 ARG 0.002 0.000 ARG C 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 216 time to evaluate : 1.944 Fit side-chains REVERT: A 209 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.4832 (ttt90) REVERT: A 294 THR cc_start: 0.8538 (m) cc_final: 0.8282 (t) REVERT: A 456 ARG cc_start: 0.7503 (mtm110) cc_final: 0.6893 (mmm160) REVERT: A 482 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7390 (ttt90) REVERT: B 259 SER cc_start: 0.8092 (m) cc_final: 0.7848 (p) REVERT: B 278 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8073 (mp10) REVERT: B 402 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8879 (p) REVERT: B 409 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8507 (mt0) REVERT: B 411 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7683 (tt) REVERT: B 482 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7733 (ttt90) REVERT: C 209 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.4715 (ttt90) REVERT: C 233 ILE cc_start: 0.5286 (OUTLIER) cc_final: 0.4795 (mp) REVERT: C 248 ASN cc_start: 0.5739 (OUTLIER) cc_final: 0.5414 (t0) REVERT: C 278 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: C 456 ARG cc_start: 0.7104 (mtt-85) cc_final: 0.6526 (mmm160) REVERT: D 209 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.4695 (ttt90) REVERT: D 278 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: D 302 TYR cc_start: 0.8826 (t80) cc_final: 0.8531 (t80) REVERT: D 312 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7906 (ttpt) REVERT: D 456 ARG cc_start: 0.7484 (mtm110) cc_final: 0.6852 (mmm160) REVERT: E 278 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: E 370 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7435 (p0) REVERT: E 402 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8856 (p) REVERT: E 409 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8436 (mt0) REVERT: E 411 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7803 (tt) REVERT: F 162 MET cc_start: 0.7692 (ttp) cc_final: 0.7306 (ttm) REVERT: F 233 ILE cc_start: 0.5256 (OUTLIER) cc_final: 0.4739 (mp) REVERT: F 278 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7560 (mp10) outliers start: 94 outliers final: 62 residues processed: 283 average time/residue: 1.1831 time to fit residues: 373.1202 Evaluate side-chains 284 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 204 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 452 VAL Chi-restraints excluded: chain F residue 508 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 GLN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN E 417 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.140860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110599 restraints weight = 20768.507| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.17 r_work: 0.3301 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16212 Z= 0.325 Angle : 0.710 10.337 21996 Z= 0.354 Chirality : 0.049 0.154 2586 Planarity : 0.004 0.046 2856 Dihedral : 5.006 22.667 2226 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.97 % Allowed : 22.24 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2094 helix: -2.73 (0.25), residues: 258 sheet: 0.42 (0.21), residues: 588 loop : -1.10 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 222 HIS 0.004 0.001 HIS D 441 PHE 0.012 0.002 PHE E 451 TYR 0.013 0.001 TYR A 302 ARG 0.002 0.000 ARG D 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.01 seconds wall clock time: 114 minutes 54.73 seconds (6894.73 seconds total)