Starting phenix.real_space_refine on Sat Mar 16 23:27:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0i_20999/03_2024/6v0i_20999.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0i_20999/03_2024/6v0i_20999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0i_20999/03_2024/6v0i_20999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0i_20999/03_2024/6v0i_20999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0i_20999/03_2024/6v0i_20999.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0i_20999/03_2024/6v0i_20999.pdb" } resolution = 3.43 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= 0.007 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 "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 "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 "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 "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 "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" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.39, per 1000 atoms: 0.53 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: 5.13 Conformation dependent library (CDL) restraints added in 2.7 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: 60 helices and 30 sheets defined 18.5% alpha, 33.3% 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 211 through 215 Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.207A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 248' Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.674A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.223A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.282A pdb=" N LEU A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 243 through 248 removed outlier: 4.207A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 248' Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.224A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 4.282A pdb=" N LEU B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 243 through 248 removed outlier: 4.206A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 248' Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.225A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.281A pdb=" N LEU C 386 " --> pdb=" O GLY C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU C 444 " --> pdb=" O GLN C 440 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 243 through 248 removed outlier: 4.206A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 248' Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.674A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.224A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 4.281A pdb=" N LEU D 386 " --> pdb=" O GLY D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 438 through 446 removed outlier: 4.242A pdb=" N GLU D 443 " --> pdb=" O PRO D 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU D 444 " --> pdb=" O GLN D 440 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'E' and resid 243 through 248 removed outlier: 4.206A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 248' Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.674A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU E 334 " --> pdb=" O SER E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 removed outlier: 4.223A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 4.283A pdb=" N LEU E 386 " --> pdb=" O GLY E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 389 No H-bonds generated for 'chain 'E' and resid 387 through 389' Processing helix chain 'E' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU E 443 " --> pdb=" O PRO E 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU E 444 " --> pdb=" O GLN E 440 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 243 through 248 removed outlier: 4.205A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 243 through 248' Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.674A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 361 removed outlier: 4.224A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 removed outlier: 4.281A pdb=" N LEU F 386 " --> pdb=" O GLY F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 389 No H-bonds generated for 'chain 'F' and resid 387 through 389' Processing helix chain 'F' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU F 443 " --> pdb=" O PRO F 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU F 444 " --> pdb=" O GLN F 440 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) 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: 6.165A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.182A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.358A 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: 3.609A pdb=" N ILE A 481 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL A 421 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA A 436 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 495 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 458 through 460 Processing sheet with id=AA7, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.166A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 228 through 229 Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.183A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.358A 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: 3.610A pdb=" N ILE B 481 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 421 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA B 436 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 495 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 458 through 460 Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.165A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=AB5, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.183A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.358A 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: 3.609A pdb=" N ILE C 481 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL C 421 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA C 436 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 495 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 458 through 460 Processing sheet with id=AB8, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.165A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 228 through 229 Processing sheet with id=AC1, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.182A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.358A 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: 3.610A pdb=" N ILE D 481 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL D 421 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA D 436 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 495 " --> pdb=" O THR D 396 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AC4, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.166A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 228 through 229 Processing sheet with id=AC6, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.183A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.358A 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: 3.610A pdb=" N ILE E 481 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL E 421 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA E 436 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR E 495 " --> pdb=" O THR E 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 458 through 460 Processing sheet with id=AC9, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.166A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.799A 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: 6.183A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.359A 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: 3.610A pdb=" N ILE F 481 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL F 421 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA F 436 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 495 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 458 through 460 564 hydrogen bonds defined for protein. 1386 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: 5.12 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4969 1.34 - 1.45: 1890 1.45 - 1.57: 9305 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 16212 Sorted by residual: bond pdb=" CB VAL C 307 " pdb=" CG1 VAL C 307 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.55e+00 bond pdb=" CB VAL B 307 " pdb=" CG1 VAL B 307 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.54e+00 bond pdb=" CB VAL D 307 " pdb=" CG1 VAL D 307 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.52e+00 bond pdb=" CB VAL F 307 " pdb=" CG1 VAL F 307 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB VAL A 307 " pdb=" CG1 VAL A 307 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.45e+00 ... (remaining 16207 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.18: 379 105.18 - 112.39: 8182 112.39 - 119.61: 5484 119.61 - 126.83: 7787 126.83 - 134.05: 164 Bond angle restraints: 21996 Sorted by residual: angle pdb=" N SER B 472 " pdb=" CA SER B 472 " pdb=" C SER B 472 " ideal model delta sigma weight residual 109.24 103.07 6.17 1.51e+00 4.39e-01 1.67e+01 angle pdb=" N SER D 472 " pdb=" CA SER D 472 " pdb=" C SER D 472 " ideal model delta sigma weight residual 109.24 103.09 6.15 1.51e+00 4.39e-01 1.66e+01 angle pdb=" N SER A 472 " pdb=" CA SER A 472 " pdb=" C SER A 472 " ideal model delta sigma weight residual 109.24 103.09 6.15 1.51e+00 4.39e-01 1.66e+01 angle pdb=" N SER E 472 " pdb=" CA SER E 472 " pdb=" C SER E 472 " ideal model delta sigma weight residual 109.24 103.12 6.12 1.51e+00 4.39e-01 1.64e+01 angle pdb=" N SER F 472 " pdb=" CA SER F 472 " pdb=" C SER F 472 " ideal model delta sigma weight residual 109.24 103.13 6.11 1.51e+00 4.39e-01 1.64e+01 ... (remaining 21991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 9299 15.73 - 31.47: 421 31.47 - 47.20: 96 47.20 - 62.94: 12 62.94 - 78.67: 24 Dihedral angle restraints: 9852 sinusoidal: 3900 harmonic: 5952 Sorted by residual: dihedral pdb=" CA LEU B 411 " pdb=" C LEU B 411 " pdb=" N ILE B 412 " pdb=" CA ILE B 412 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU D 411 " pdb=" C LEU D 411 " pdb=" N ILE D 412 " pdb=" CA ILE D 412 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU C 411 " pdb=" C LEU C 411 " pdb=" N ILE C 412 " pdb=" CA ILE C 412 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1701 0.062 - 0.124: 654 0.124 - 0.186: 185 0.186 - 0.248: 34 0.248 - 0.310: 12 Chirality restraints: 2586 Sorted by residual: 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 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ASN D 338 " pdb=" N ASN D 338 " pdb=" C ASN D 338 " pdb=" CB ASN D 338 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 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 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 2583 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 336 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C ARG F 336 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG F 336 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU F 337 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 336 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C ARG D 336 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG D 336 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU D 337 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 336 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C ARG A 336 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG A 336 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 337 " -0.017 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3555 2.80 - 3.32: 13294 3.32 - 3.85: 24404 3.85 - 4.37: 28003 4.37 - 4.90: 50216 Nonbonded interactions: 119472 Sorted by model distance: nonbonded pdb=" O SER B 330 " pdb=" OG1 THR B 333 " model vdw 2.274 2.440 nonbonded pdb=" O SER F 330 " pdb=" OG1 THR F 333 " model vdw 2.274 2.440 nonbonded pdb=" O SER C 330 " pdb=" OG1 THR C 333 " model vdw 2.274 2.440 nonbonded pdb=" O SER A 330 " pdb=" OG1 THR A 333 " model vdw 2.274 2.440 nonbonded pdb=" O SER D 330 " pdb=" OG1 THR D 333 " model vdw 2.274 2.440 ... (remaining 119467 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.240 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 40.940 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.007 0.062 16212 Z= 0.469 Angle : 1.179 10.034 21996 Z= 0.651 Chirality : 0.073 0.310 2586 Planarity : 0.009 0.056 2856 Dihedral : 10.964 78.672 6048 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -2.32 (0.16), residues: 2094 helix: -1.53 (0.33), residues: 234 sheet: -1.17 (0.20), residues: 612 loop : -1.77 (0.14), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.004 TRP F 476 HIS 0.008 0.003 HIS A 441 PHE 0.039 0.005 PHE C 221 TYR 0.012 0.003 TYR C 498 ARG 0.007 0.001 ARG F 336 *********************** 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 462 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 TYR cc_start: 0.8691 (t80) cc_final: 0.8476 (t80) REVERT: A 396 THR cc_start: 0.8572 (m) cc_final: 0.8280 (p) REVERT: B 166 GLN cc_start: 0.8061 (mt0) cc_final: 0.7433 (mt0) REVERT: B 240 LEU cc_start: 0.7614 (tt) cc_final: 0.7350 (tp) REVERT: B 267 THR cc_start: 0.8822 (t) cc_final: 0.8297 (t) REVERT: B 453 VAL cc_start: 0.9438 (t) cc_final: 0.9153 (p) REVERT: C 240 LEU cc_start: 0.7727 (tt) cc_final: 0.7520 (tp) REVERT: C 324 GLU cc_start: 0.8121 (pt0) cc_final: 0.7880 (pt0) REVERT: C 482 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7607 (ttt180) REVERT: D 396 THR cc_start: 0.8587 (m) cc_final: 0.8272 (p) REVERT: E 166 GLN cc_start: 0.8063 (mt0) cc_final: 0.7425 (mt0) REVERT: E 240 LEU cc_start: 0.7619 (tt) cc_final: 0.7379 (tp) REVERT: E 267 THR cc_start: 0.8806 (t) cc_final: 0.8232 (t) REVERT: E 453 VAL cc_start: 0.9441 (t) cc_final: 0.9154 (p) REVERT: F 324 GLU cc_start: 0.8101 (pt0) cc_final: 0.7851 (pt0) REVERT: F 363 THR cc_start: 0.7519 (m) cc_final: 0.7250 (m) REVERT: F 401 GLU cc_start: 0.7983 (tt0) cc_final: 0.7634 (tt0) REVERT: F 403 TYR cc_start: 0.9341 (m-80) cc_final: 0.8890 (m-80) REVERT: F 482 ARG cc_start: 0.7864 (ttt-90) cc_final: 0.7616 (ttt180) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.3403 time to fit residues: 216.1274 Evaluate side-chains 236 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.4980 chunk 159 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 190 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 316 ASN A 409 GLN A 440 GLN A 454 ASN B 164 HIS B 316 ASN B 345 ASN B 441 HIS B 454 ASN C 164 HIS C 316 ASN C 345 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 316 ASN D 345 ASN D 409 GLN D 440 GLN D 454 ASN E 164 HIS E 316 ASN E 345 ASN E 354 ASN E 441 HIS E 454 ASN F 164 HIS F 166 GLN F 316 ASN F 345 ASN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2622 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= 0.188 Angle : 0.637 7.270 21996 Z= 0.330 Chirality : 0.047 0.151 2586 Planarity : 0.005 0.043 2856 Dihedral : 5.160 20.738 2226 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.28 % Allowed : 11.83 % Favored : 85.89 % 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: -1.67 (0.16), residues: 2094 helix: -2.00 (0.29), residues: 204 sheet: -0.26 (0.21), residues: 576 loop : -1.40 (0.14), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 222 HIS 0.009 0.001 HIS C 441 PHE 0.015 0.002 PHE E 364 TYR 0.010 0.001 TYR C 403 ARG 0.006 0.001 ARG C 279 *********************** 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 304 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 264 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.7995 (tt) cc_final: 0.7547 (tp) REVERT: A 396 THR cc_start: 0.8502 (m) cc_final: 0.8213 (p) REVERT: B 166 GLN cc_start: 0.8045 (mt0) cc_final: 0.7469 (mt0) REVERT: B 224 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8086 (m) REVERT: B 267 THR cc_start: 0.8951 (t) cc_final: 0.8529 (t) REVERT: B 342 GLU cc_start: 0.8009 (pm20) cc_final: 0.7598 (pm20) REVERT: C 468 PHE cc_start: 0.7753 (t80) cc_final: 0.7514 (t80) REVERT: C 482 ARG cc_start: 0.7992 (ttt-90) cc_final: 0.7724 (ttt180) REVERT: D 190 TYR cc_start: 0.8712 (t80) cc_final: 0.8487 (t80) REVERT: D 240 LEU cc_start: 0.8011 (tt) cc_final: 0.7583 (tp) REVERT: D 396 THR cc_start: 0.8525 (m) cc_final: 0.8233 (p) REVERT: D 491 MET cc_start: 0.8239 (tpt) cc_final: 0.7807 (tpt) REVERT: E 224 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8087 (m) REVERT: E 267 THR cc_start: 0.8935 (t) cc_final: 0.8714 (m) REVERT: E 342 GLU cc_start: 0.8008 (pm20) cc_final: 0.7618 (pm20) REVERT: F 166 GLN cc_start: 0.8008 (mt0) cc_final: 0.7727 (mt0) REVERT: F 482 ARG cc_start: 0.7989 (ttt-90) cc_final: 0.7759 (ttt180) outliers start: 40 outliers final: 21 residues processed: 289 average time/residue: 0.2590 time to fit residues: 112.8365 Evaluate side-chains 230 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 409 GLN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 501 LEU 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: 3.9990 chunk 59 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 189 optimal weight: 0.0770 chunk 65 optimal weight: 0.0770 chunk 153 optimal weight: 2.9990 overall best weight: 0.8298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 454 ASN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16212 Z= 0.244 Angle : 0.631 8.510 21996 Z= 0.323 Chirality : 0.047 0.152 2586 Planarity : 0.004 0.041 2856 Dihedral : 5.132 21.232 2226 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.41 % Allowed : 13.03 % Favored : 83.56 % 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: -1.59 (0.16), residues: 2094 helix: -2.03 (0.28), residues: 240 sheet: 0.02 (0.22), residues: 576 loop : -1.42 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 222 HIS 0.008 0.001 HIS C 441 PHE 0.024 0.002 PHE B 468 TYR 0.011 0.001 TYR C 403 ARG 0.004 0.001 ARG C 279 *********************** 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 278 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 218 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8050 (tt) cc_final: 0.7649 (tp) REVERT: A 396 THR cc_start: 0.8617 (m) cc_final: 0.8312 (p) REVERT: A 491 MET cc_start: 0.8302 (tpt) cc_final: 0.7936 (tpt) REVERT: B 166 GLN cc_start: 0.8033 (mt0) cc_final: 0.7577 (mt0) REVERT: B 224 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8069 (m) REVERT: B 267 THR cc_start: 0.8943 (t) cc_final: 0.8596 (t) REVERT: B 426 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9061 (tp) REVERT: C 426 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9093 (tp) REVERT: D 240 LEU cc_start: 0.8266 (tt) cc_final: 0.7909 (tp) REVERT: D 456 ARG cc_start: 0.7241 (mtm110) cc_final: 0.7034 (mmp80) REVERT: D 491 MET cc_start: 0.8337 (tpt) cc_final: 0.8000 (tpt) REVERT: E 224 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8099 (m) REVERT: E 426 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9087 (tp) REVERT: F 325 MET cc_start: 0.8583 (mtm) cc_final: 0.8275 (mtm) REVERT: F 426 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9122 (tp) REVERT: F 482 ARG cc_start: 0.8057 (ttt-90) cc_final: 0.7792 (ttt180) outliers start: 60 outliers final: 36 residues processed: 267 average time/residue: 0.2659 time to fit residues: 106.5937 Evaluate side-chains 228 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 501 LEU 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: 5.9990 chunk 143 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN D 409 GLN F 166 GLN F 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16212 Z= 0.242 Angle : 0.604 9.438 21996 Z= 0.310 Chirality : 0.047 0.155 2586 Planarity : 0.004 0.043 2856 Dihedral : 5.108 21.907 2226 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.53 % Allowed : 14.05 % Favored : 82.42 % 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 (0.16), residues: 2094 helix: -1.98 (0.29), residues: 240 sheet: 0.13 (0.22), residues: 576 loop : -1.32 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 222 HIS 0.007 0.001 HIS C 441 PHE 0.017 0.002 PHE A 468 TYR 0.009 0.001 TYR C 403 ARG 0.003 0.001 ARG F 279 *********************** 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 264 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 202 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.7946 (tt) cc_final: 0.7564 (tp) REVERT: A 396 THR cc_start: 0.8600 (m) cc_final: 0.8256 (p) REVERT: A 482 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7783 (ptt90) REVERT: A 491 MET cc_start: 0.8468 (tpt) cc_final: 0.8139 (tpt) REVERT: A 501 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8838 (tp) REVERT: B 166 GLN cc_start: 0.7983 (mt0) cc_final: 0.7536 (mt0) REVERT: B 267 THR cc_start: 0.8907 (t) cc_final: 0.8558 (t) REVERT: B 454 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.7190 (m-40) REVERT: C 426 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9023 (tp) REVERT: C 444 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8262 (tt) REVERT: D 240 LEU cc_start: 0.8192 (tt) cc_final: 0.7855 (tp) REVERT: D 396 THR cc_start: 0.8619 (m) cc_final: 0.8278 (p) REVERT: D 482 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7767 (ptt90) REVERT: D 491 MET cc_start: 0.8430 (tpt) cc_final: 0.8093 (tpt) REVERT: E 454 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.7178 (m-40) REVERT: F 325 MET cc_start: 0.8496 (mtm) cc_final: 0.8164 (mtm) REVERT: F 426 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9106 (tp) REVERT: F 444 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8255 (tt) REVERT: F 482 ARG cc_start: 0.8066 (ttt-90) cc_final: 0.7763 (ttt180) outliers start: 62 outliers final: 41 residues processed: 256 average time/residue: 0.2844 time to fit residues: 107.4013 Evaluate side-chains 237 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 187 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 501 LEU 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 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 409 GLN Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 501 LEU 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: 0.9980 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4048 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= 0.335 Angle : 0.649 10.568 21996 Z= 0.335 Chirality : 0.048 0.170 2586 Planarity : 0.004 0.043 2856 Dihedral : 5.352 22.959 2226 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.01 % Allowed : 12.57 % Favored : 82.42 % 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: -1.40 (0.17), residues: 2094 helix: -2.05 (0.29), residues: 240 sheet: 0.05 (0.20), residues: 672 loop : -1.28 (0.15), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 222 HIS 0.007 0.001 HIS F 441 PHE 0.025 0.003 PHE A 451 TYR 0.009 0.001 TYR D 271 ARG 0.005 0.001 ARG E 220 *********************** 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 289 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 201 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: A 240 LEU cc_start: 0.7961 (tt) cc_final: 0.7578 (tp) REVERT: A 396 THR cc_start: 0.8680 (m) cc_final: 0.8437 (p) REVERT: A 444 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8435 (tt) REVERT: B 166 GLN cc_start: 0.7987 (mt0) cc_final: 0.7594 (mt0) REVERT: B 267 THR cc_start: 0.8894 (t) cc_final: 0.8579 (t) REVERT: B 328 ASP cc_start: 0.6410 (t0) cc_final: 0.6194 (t0) REVERT: B 396 THR cc_start: 0.8886 (m) cc_final: 0.8500 (p) REVERT: B 411 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8899 (tp) REVERT: B 454 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7470 (m-40) REVERT: B 456 ARG cc_start: 0.6183 (mmt180) cc_final: 0.5769 (mmp-170) REVERT: C 350 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.6063 (pp) REVERT: C 426 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9054 (tp) REVERT: C 444 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8383 (tt) REVERT: D 240 LEU cc_start: 0.8237 (tt) cc_final: 0.7902 (tp) REVERT: D 396 THR cc_start: 0.8742 (m) cc_final: 0.8523 (p) REVERT: D 491 MET cc_start: 0.8397 (tpt) cc_final: 0.8183 (tpt) REVERT: E 328 ASP cc_start: 0.6410 (t0) cc_final: 0.6199 (t0) REVERT: E 411 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8898 (tp) REVERT: E 454 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7411 (m-40) REVERT: E 456 ARG cc_start: 0.6237 (mmt180) cc_final: 0.5823 (mmp-170) REVERT: F 325 MET cc_start: 0.8596 (mtm) cc_final: 0.8372 (mtm) REVERT: F 426 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9067 (tp) REVERT: F 444 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8429 (tt) outliers start: 88 outliers final: 56 residues processed: 277 average time/residue: 0.2577 time to fit residues: 107.2534 Evaluate side-chains 243 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 177 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 445 VAL 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 339 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 508 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 203 optimal weight: 0.0000 chunk 168 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16212 Z= 0.181 Angle : 0.590 11.320 21996 Z= 0.298 Chirality : 0.046 0.149 2586 Planarity : 0.004 0.043 2856 Dihedral : 4.838 20.922 2226 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.13 % Allowed : 14.96 % Favored : 81.91 % 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: -1.33 (0.17), residues: 2094 helix: -1.96 (0.29), residues: 240 sheet: 0.09 (0.20), residues: 672 loop : -1.23 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 222 HIS 0.007 0.001 HIS C 441 PHE 0.011 0.001 PHE A 451 TYR 0.008 0.001 TYR C 403 ARG 0.003 0.000 ARG D 442 *********************** 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 256 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 201 time to evaluate : 1.901 Fit side-chains REVERT: A 240 LEU cc_start: 0.7829 (tt) cc_final: 0.7505 (tp) REVERT: A 396 THR cc_start: 0.8618 (m) cc_final: 0.8369 (p) REVERT: A 409 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8064 (mm110) REVERT: A 482 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7734 (ptt90) REVERT: B 397 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8634 (pp) REVERT: B 454 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7374 (m-40) REVERT: C 204 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7520 (p0) REVERT: C 426 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8927 (tp) REVERT: D 240 LEU cc_start: 0.8087 (tt) cc_final: 0.7804 (tp) REVERT: D 482 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7756 (ptt90) REVERT: D 491 MET cc_start: 0.8318 (tpt) cc_final: 0.8019 (tpt) REVERT: E 397 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8687 (pp) REVERT: E 454 ASN cc_start: 0.7616 (OUTLIER) cc_final: 0.7382 (m-40) REVERT: E 456 ARG cc_start: 0.6256 (mmt180) cc_final: 0.5875 (mmp-170) REVERT: F 325 MET cc_start: 0.8481 (mtm) cc_final: 0.8230 (mtm) REVERT: F 426 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9048 (tp) REVERT: F 444 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8356 (tt) outliers start: 55 outliers final: 33 residues processed: 244 average time/residue: 0.2708 time to fit residues: 98.1971 Evaluate side-chains 230 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 0.0000 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4258 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= 0.242 Angle : 0.612 11.883 21996 Z= 0.308 Chirality : 0.047 0.154 2586 Planarity : 0.004 0.046 2856 Dihedral : 4.934 21.230 2226 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.47 % Allowed : 14.96 % Favored : 81.57 % 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: -1.31 (0.17), residues: 2094 helix: -1.99 (0.29), residues: 240 sheet: 0.05 (0.20), residues: 672 loop : -1.17 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 222 HIS 0.007 0.001 HIS F 441 PHE 0.026 0.002 PHE B 468 TYR 0.007 0.001 TYR C 403 ARG 0.003 0.001 ARG B 220 *********************** 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 248 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 187 time to evaluate : 1.865 Fit side-chains REVERT: A 240 LEU cc_start: 0.7847 (tt) cc_final: 0.7521 (tp) REVERT: A 396 THR cc_start: 0.8675 (m) cc_final: 0.8387 (p) REVERT: A 409 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8048 (mm110) REVERT: A 482 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7722 (ptt90) REVERT: B 397 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8746 (pp) REVERT: B 454 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7446 (m-40) REVERT: C 166 GLN cc_start: 0.8315 (mm110) cc_final: 0.7901 (mp10) REVERT: C 204 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7360 (p0) REVERT: C 350 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6239 (pp) REVERT: D 240 LEU cc_start: 0.8066 (tt) cc_final: 0.7775 (tp) REVERT: D 491 MET cc_start: 0.8493 (tpt) cc_final: 0.8196 (tpt) REVERT: E 454 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7405 (m-40) REVERT: E 456 ARG cc_start: 0.6253 (mmt180) cc_final: 0.5889 (mmp-170) REVERT: F 325 MET cc_start: 0.8525 (mtm) cc_final: 0.8273 (mtm) REVERT: F 444 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8506 (tt) outliers start: 61 outliers final: 47 residues processed: 234 average time/residue: 0.3050 time to fit residues: 106.7298 Evaluate side-chains 237 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 182 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 307 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 0.0030 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4337 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= 0.180 Angle : 0.590 13.112 21996 Z= 0.293 Chirality : 0.046 0.145 2586 Planarity : 0.004 0.048 2856 Dihedral : 4.683 20.329 2226 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.30 % Allowed : 15.24 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2094 helix: -1.91 (0.29), residues: 240 sheet: 0.09 (0.20), residues: 666 loop : -1.14 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 222 HIS 0.007 0.001 HIS F 441 PHE 0.014 0.001 PHE E 451 TYR 0.008 0.001 TYR C 403 ARG 0.003 0.000 ARG F 209 *********************** 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 244 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 186 time to evaluate : 1.863 Fit side-chains REVERT: A 240 LEU cc_start: 0.7786 (tt) cc_final: 0.7516 (tp) REVERT: B 365 GLU cc_start: 0.7904 (tp30) cc_final: 0.7577 (tt0) REVERT: B 397 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8571 (pp) REVERT: B 454 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7390 (m-40) REVERT: C 166 GLN cc_start: 0.8277 (mm110) cc_final: 0.7862 (mp10) REVERT: C 204 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7357 (p0) REVERT: D 240 LEU cc_start: 0.7769 (tt) cc_final: 0.7506 (tp) REVERT: D 491 MET cc_start: 0.8355 (tpt) cc_final: 0.8086 (tpt) REVERT: E 365 GLU cc_start: 0.7916 (tp30) cc_final: 0.7570 (tt0) REVERT: E 454 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7329 (m-40) REVERT: F 325 MET cc_start: 0.8444 (mtm) cc_final: 0.8169 (mtm) REVERT: F 444 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8510 (tt) outliers start: 58 outliers final: 40 residues processed: 232 average time/residue: 0.2775 time to fit residues: 95.0914 Evaluate side-chains 225 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 180 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 367 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 350 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 501 LEU 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: 3.9990 chunk 188 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16212 Z= 0.338 Angle : 0.659 11.326 21996 Z= 0.332 Chirality : 0.048 0.163 2586 Planarity : 0.004 0.044 2856 Dihedral : 5.199 22.936 2226 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.53 % Allowed : 14.79 % Favored : 81.68 % 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: -1.37 (0.17), residues: 2094 helix: -2.09 (0.29), residues: 240 sheet: -0.07 (0.20), residues: 672 loop : -1.14 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 222 HIS 0.007 0.001 HIS C 441 PHE 0.022 0.002 PHE C 468 TYR 0.008 0.001 TYR D 271 ARG 0.005 0.001 ARG B 220 *********************** 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 249 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 187 time to evaluate : 1.966 Fit side-chains REVERT: A 240 LEU cc_start: 0.7864 (tt) cc_final: 0.7537 (tp) REVERT: B 454 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7505 (m-40) REVERT: C 166 GLN cc_start: 0.8286 (mm110) cc_final: 0.7866 (mp10) REVERT: C 204 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7496 (p0) REVERT: D 240 LEU cc_start: 0.7930 (tt) cc_final: 0.7620 (tp) REVERT: E 209 ARG cc_start: 0.6358 (mmt180) cc_final: 0.5799 (mmt180) REVERT: E 454 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7498 (m-40) REVERT: F 325 MET cc_start: 0.8567 (mtm) cc_final: 0.8332 (mtm) REVERT: F 444 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8577 (tt) REVERT: F 482 ARG cc_start: 0.8257 (ttt-90) cc_final: 0.8050 (ttt180) outliers start: 62 outliers final: 53 residues processed: 237 average time/residue: 0.2783 time to fit residues: 97.7870 Evaluate side-chains 235 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 178 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 307 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 444 LEU 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: 2.9990 chunk 121 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16212 Z= 0.340 Angle : 0.672 10.635 21996 Z= 0.339 Chirality : 0.048 0.157 2586 Planarity : 0.004 0.047 2856 Dihedral : 5.329 22.884 2226 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.53 % Allowed : 14.79 % Favored : 81.68 % 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: -1.48 (0.17), residues: 2094 helix: -2.18 (0.28), residues: 240 sheet: -0.22 (0.20), residues: 684 loop : -1.16 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 222 HIS 0.007 0.001 HIS C 441 PHE 0.022 0.002 PHE E 451 TYR 0.008 0.001 TYR D 271 ARG 0.005 0.001 ARG B 220 ********************** 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 246 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 184 time to evaluate : 1.832 Fit side-chains revert: symmetry clash REVERT: A 240 LEU cc_start: 0.7842 (tt) cc_final: 0.7521 (tp) REVERT: A 409 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8119 (mm110) REVERT: B 365 GLU cc_start: 0.7942 (tp30) cc_final: 0.7618 (tt0) REVERT: B 396 THR cc_start: 0.8907 (m) cc_final: 0.8658 (p) REVERT: B 454 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7563 (m-40) REVERT: C 166 GLN cc_start: 0.8272 (mm110) cc_final: 0.7844 (mp10) REVERT: C 204 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7458 (p0) REVERT: D 240 LEU cc_start: 0.7973 (tt) cc_final: 0.7676 (tp) REVERT: D 501 LEU cc_start: 0.9041 (tt) cc_final: 0.8830 (tp) REVERT: E 209 ARG cc_start: 0.6345 (mmt180) cc_final: 0.5843 (mmt180) REVERT: E 454 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7513 (m-40) REVERT: F 444 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8613 (tt) outliers start: 62 outliers final: 55 residues processed: 232 average time/residue: 0.2855 time to fit residues: 98.4247 Evaluate side-chains 239 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 179 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 307 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 444 LEU 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: 0.8980 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 0.2980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.089600 restraints weight = 22774.174| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.33 r_work: 0.2845 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16212 Z= 0.190 Angle : 0.611 11.275 21996 Z= 0.306 Chirality : 0.046 0.140 2586 Planarity : 0.004 0.049 2856 Dihedral : 4.876 21.010 2226 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.24 % Allowed : 15.24 % Favored : 81.51 % 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: -1.37 (0.17), residues: 2094 helix: -2.04 (0.28), residues: 240 sheet: -0.04 (0.20), residues: 666 loop : -1.16 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 222 HIS 0.007 0.001 HIS C 441 PHE 0.026 0.002 PHE C 468 TYR 0.007 0.001 TYR C 403 ARG 0.003 0.000 ARG C 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3334.86 seconds wall clock time: 60 minutes 51.72 seconds (3651.72 seconds total)