Starting phenix.real_space_refine on Thu Feb 15 08:41:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlq_22377/02_2024/7jlq_22377.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlq_22377/02_2024/7jlq_22377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlq_22377/02_2024/7jlq_22377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlq_22377/02_2024/7jlq_22377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlq_22377/02_2024/7jlq_22377.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlq_22377/02_2024/7jlq_22377.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 7725 2.51 5 N 1962 2.21 5 O 1947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 506": "NH1" <-> "NH2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 506": "NH1" <-> "NH2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11700 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3900 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 17, 'TRANS': 456} Chain breaks: 1 Chain: "B" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3900 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 17, 'TRANS': 456} Chain breaks: 1 Chain: "C" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3900 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 17, 'TRANS': 456} Chain breaks: 1 Time building chain proxies: 6.40, per 1000 atoms: 0.55 Number of scatterers: 11700 At special positions: 0 Unit cell: (130.41, 123.606, 92.988, 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 66 16.00 O 1947 8.00 N 1962 7.00 C 7725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 122 " distance=2.03 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: 4.12 Conformation dependent library (CDL) restraints added in 2.4 seconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 9 sheets defined 73.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.658A pdb=" N HIS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 86 removed outlier: 3.820A pdb=" N MET A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 4.336A pdb=" N ALA A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 116' Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 132 through 166 removed outlier: 3.852A pdb=" N ILE A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.514A pdb=" N THR A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.789A pdb=" N ARG A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY A 276 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 317 Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 346 through 357 removed outlier: 3.632A pdb=" N ARG A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 370 through 398 removed outlier: 3.581A pdb=" N VAL A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 407 through 422 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.711A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.820A pdb=" N GLN A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.628A pdb=" N ARG A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 481 through 493 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 508 removed outlier: 3.546A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 removed outlier: 3.658A pdb=" N HIS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 86 removed outlier: 3.820A pdb=" N MET B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 4.336A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 116' Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 132 through 166 removed outlier: 3.851A pdb=" N ILE B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.516A pdb=" N THR B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.789A pdb=" N ARG B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY B 276 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY B 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 317 Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 346 through 357 removed outlier: 3.632A pdb=" N ARG B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 398 removed outlier: 3.581A pdb=" N VAL B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 407 through 422 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.711A pdb=" N ARG B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.821A pdb=" N GLN B 453 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.628A pdb=" N ARG B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 Processing helix chain 'B' and resid 481 through 493 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 497 through 508 removed outlier: 3.545A pdb=" N ILE B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 removed outlier: 3.659A pdb=" N HIS C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 86 removed outlier: 3.820A pdb=" N MET C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 116 removed outlier: 4.336A pdb=" N ALA C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 116' Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 132 through 166 removed outlier: 3.851A pdb=" N ILE C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU C 159 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.515A pdb=" N THR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 215 through 225 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.789A pdb=" N ARG C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C 276 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY C 277 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 317 Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 333 through 340 Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.632A pdb=" N ARG C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 Processing helix chain 'C' and resid 370 through 398 removed outlier: 3.581A pdb=" N VAL C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 407 through 422 Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.712A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.821A pdb=" N GLN C 453 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 removed outlier: 3.627A pdb=" N ARG C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 481 Processing helix chain 'C' and resid 481 through 493 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 497 through 508 removed outlier: 3.546A pdb=" N ILE C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 512 Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AA5, first strand: chain 'B' and resid 330 through 332 Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 512 Processing sheet with id=AA7, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AA8, first strand: chain 'C' and resid 330 through 332 Processing sheet with id=AA9, first strand: chain 'C' and resid 509 through 512 696 hydrogen bonds defined for protein. 1971 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: 3.22 Time building geometry restraints manager: 4.56 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: 3635 1.34 - 1.46: 2515 1.46 - 1.57: 5790 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 12027 Sorted by residual: bond pdb=" CA PHE C 242 " pdb=" CB PHE C 242 " ideal model delta sigma weight residual 1.526 1.495 0.031 1.53e-02 4.27e+03 4.19e+00 bond pdb=" CB GLN B 120 " pdb=" CG GLN B 120 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.15e+00 bond pdb=" CB GLN A 120 " pdb=" CG GLN A 120 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.09e+00 bond pdb=" CB GLN C 120 " pdb=" CG GLN C 120 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.08e+00 bond pdb=" CB TRP B 332 " pdb=" CG TRP B 332 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.79e+00 ... (remaining 12022 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.43: 147 104.43 - 111.88: 5793 111.88 - 119.34: 4191 119.34 - 126.79: 6023 126.79 - 134.25: 184 Bond angle restraints: 16338 Sorted by residual: angle pdb=" CB GLN A 120 " pdb=" CG GLN A 120 " pdb=" CD GLN A 120 " ideal model delta sigma weight residual 112.60 119.42 -6.82 1.70e+00 3.46e-01 1.61e+01 angle pdb=" CB GLN B 120 " pdb=" CG GLN B 120 " pdb=" CD GLN B 120 " ideal model delta sigma weight residual 112.60 119.41 -6.81 1.70e+00 3.46e-01 1.60e+01 angle pdb=" CB GLN C 120 " pdb=" CG GLN C 120 " pdb=" CD GLN C 120 " ideal model delta sigma weight residual 112.60 119.40 -6.80 1.70e+00 3.46e-01 1.60e+01 angle pdb=" CA GLN C 120 " pdb=" CB GLN C 120 " pdb=" CG GLN C 120 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CA GLN B 120 " pdb=" CB GLN B 120 " pdb=" CG GLN B 120 " ideal model delta sigma weight residual 114.10 121.73 -7.63 2.00e+00 2.50e-01 1.46e+01 ... (remaining 16333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 6291 17.52 - 35.04: 579 35.04 - 52.56: 114 52.56 - 70.08: 18 70.08 - 87.60: 15 Dihedral angle restraints: 7017 sinusoidal: 2832 harmonic: 4185 Sorted by residual: dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 122 " pdb=" CB CYS C 122 " ideal model delta sinusoidal sigma weight residual -86.00 -119.71 33.71 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 122 " pdb=" CB CYS B 122 " ideal model delta sinusoidal sigma weight residual -86.00 -119.69 33.69 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 122 " pdb=" CB CYS A 122 " ideal model delta sinusoidal sigma weight residual -86.00 -119.69 33.69 1 1.00e+01 1.00e-02 1.61e+01 ... (remaining 7014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 964 0.036 - 0.071: 536 0.071 - 0.107: 246 0.107 - 0.143: 69 0.143 - 0.178: 21 Chirality restraints: 1836 Sorted by residual: chirality pdb=" CB ILE A 254 " pdb=" CA ILE A 254 " pdb=" CG1 ILE A 254 " pdb=" CG2 ILE A 254 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CB ILE B 254 " pdb=" CA ILE B 254 " pdb=" CG1 ILE B 254 " pdb=" CG2 ILE B 254 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CB ILE C 254 " pdb=" CA ILE C 254 " pdb=" CG1 ILE C 254 " pdb=" CG2 ILE C 254 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 1833 not shown) Planarity restraints: 2031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 180 " 0.018 2.00e-02 2.50e+03 1.77e-02 7.80e+00 pdb=" CG TRP C 180 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 180 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 180 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 180 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 180 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 180 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 180 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 180 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 180 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 180 " 0.019 2.00e-02 2.50e+03 1.76e-02 7.77e+00 pdb=" CG TRP A 180 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 180 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 180 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 180 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 180 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 180 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 180 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 180 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 180 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 180 " -0.019 2.00e-02 2.50e+03 1.76e-02 7.76e+00 pdb=" CG TRP B 180 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 180 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 180 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 180 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 180 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 180 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 180 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 180 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 180 " -0.005 2.00e-02 2.50e+03 ... (remaining 2028 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 432 2.70 - 3.25: 12051 3.25 - 3.80: 18486 3.80 - 4.35: 23424 4.35 - 4.90: 38982 Nonbonded interactions: 93375 Sorted by model distance: nonbonded pdb=" OH TYR C 209 " pdb=" OE2 GLU C 349 " model vdw 2.151 2.440 nonbonded pdb=" OH TYR A 209 " pdb=" OE2 GLU A 349 " model vdw 2.151 2.440 nonbonded pdb=" OH TYR B 209 " pdb=" OE2 GLU B 349 " model vdw 2.151 2.440 nonbonded pdb=" NH2 ARG B 49 " pdb=" OD1 ASN B 153 " model vdw 2.161 2.520 nonbonded pdb=" NH2 ARG A 49 " pdb=" OD1 ASN A 153 " model vdw 2.161 2.520 ... (remaining 93370 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' } 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 group one per residue 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.170 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.030 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 0.053 12027 Z= 0.461 Angle : 0.990 10.250 16338 Z= 0.549 Chirality : 0.054 0.178 1836 Planarity : 0.005 0.029 2031 Dihedral : 14.269 87.601 4296 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.71 % Allowed : 3.08 % Favored : 96.21 % 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: -1.82 (0.21), residues: 1410 helix: -0.46 (0.16), residues: 942 sheet: -2.13 (0.85), residues: 30 loop : -2.63 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP C 180 HIS 0.007 0.002 HIS A 451 PHE 0.040 0.003 PHE A 368 TYR 0.030 0.004 TYR A 471 ARG 0.005 0.001 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 411 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9175 (mt) cc_final: 0.8946 (tp) REVERT: A 79 PHE cc_start: 0.8860 (t80) cc_final: 0.8492 (t80) REVERT: A 83 LEU cc_start: 0.8269 (mt) cc_final: 0.7593 (mt) REVERT: A 226 SER cc_start: 0.8013 (m) cc_final: 0.7732 (p) REVERT: A 321 LYS cc_start: 0.7793 (tptm) cc_final: 0.7006 (mttt) REVERT: A 363 LYS cc_start: 0.7773 (mttt) cc_final: 0.7507 (mttt) REVERT: A 364 TYR cc_start: 0.8049 (t80) cc_final: 0.7783 (t80) REVERT: A 435 GLU cc_start: 0.7716 (tp30) cc_final: 0.7239 (tp30) REVERT: A 445 ILE cc_start: 0.6461 (pt) cc_final: 0.6249 (pt) REVERT: B 83 LEU cc_start: 0.8230 (mt) cc_final: 0.7923 (mt) REVERT: B 143 TRP cc_start: 0.8207 (t60) cc_final: 0.7709 (t60) REVERT: B 152 TYR cc_start: 0.8314 (t80) cc_final: 0.8038 (t80) REVERT: B 226 SER cc_start: 0.7959 (m) cc_final: 0.7738 (p) REVERT: B 364 TYR cc_start: 0.7941 (t80) cc_final: 0.7738 (t80) REVERT: B 372 LEU cc_start: 0.8949 (tp) cc_final: 0.8539 (mt) REVERT: B 445 ILE cc_start: 0.6512 (pt) cc_final: 0.6279 (pt) REVERT: B 471 TYR cc_start: 0.8585 (m-80) cc_final: 0.7338 (m-10) REVERT: C 62 MET cc_start: 0.7010 (ttp) cc_final: 0.6662 (tmm) REVERT: C 226 SER cc_start: 0.7880 (m) cc_final: 0.7679 (p) REVERT: C 471 TYR cc_start: 0.8526 (m-80) cc_final: 0.8311 (m-10) outliers start: 9 outliers final: 0 residues processed: 416 average time/residue: 0.2432 time to fit residues: 140.1811 Evaluate side-chains 228 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 0.0270 chunk 36 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 284 GLN A 288 ASN B 284 GLN B 288 ASN B 406 HIS C 284 GLN C 288 ASN C 406 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12027 Z= 0.186 Angle : 0.656 11.664 16338 Z= 0.329 Chirality : 0.042 0.180 1836 Planarity : 0.004 0.042 2031 Dihedral : 4.148 15.220 1557 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.92 % Allowed : 12.09 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1410 helix: 0.44 (0.17), residues: 942 sheet: -1.59 (0.88), residues: 30 loop : -2.07 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 267 HIS 0.006 0.001 HIS B 406 PHE 0.024 0.001 PHE B 475 TYR 0.016 0.001 TYR A 157 ARG 0.003 0.000 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 262 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9223 (mt) cc_final: 0.8946 (tp) REVERT: A 83 LEU cc_start: 0.8259 (mt) cc_final: 0.7938 (mt) REVERT: A 281 GLU cc_start: 0.8834 (tt0) cc_final: 0.8205 (pt0) REVERT: A 310 LEU cc_start: 0.7042 (mt) cc_final: 0.6707 (mt) REVERT: B 143 TRP cc_start: 0.8010 (t60) cc_final: 0.7412 (t60) REVERT: B 157 TYR cc_start: 0.7066 (m-80) cc_final: 0.6830 (m-80) REVERT: B 422 ARG cc_start: 0.7717 (mtp180) cc_final: 0.7470 (mtp180) REVERT: B 471 TYR cc_start: 0.8389 (m-80) cc_final: 0.6883 (m-10) REVERT: B 505 PHE cc_start: 0.7845 (m-80) cc_final: 0.7643 (m-10) REVERT: C 62 MET cc_start: 0.7213 (ttp) cc_final: 0.6552 (tmm) REVERT: C 72 GLN cc_start: 0.8362 (mt0) cc_final: 0.8161 (mt0) REVERT: C 75 PHE cc_start: 0.8117 (t80) cc_final: 0.7772 (t80) REVERT: C 81 THR cc_start: 0.8904 (p) cc_final: 0.8638 (t) REVERT: C 172 MET cc_start: 0.7693 (ppp) cc_final: 0.7426 (ppp) outliers start: 37 outliers final: 16 residues processed: 287 average time/residue: 0.2036 time to fit residues: 86.0815 Evaluate side-chains 219 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 216 GLN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12027 Z= 0.183 Angle : 0.606 11.137 16338 Z= 0.307 Chirality : 0.040 0.137 1836 Planarity : 0.004 0.052 2031 Dihedral : 4.147 17.476 1557 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.16 % Allowed : 14.93 % 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: -0.21 (0.22), residues: 1410 helix: 0.69 (0.17), residues: 948 sheet: -1.26 (0.90), residues: 30 loop : -1.85 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 143 HIS 0.003 0.001 HIS A 194 PHE 0.020 0.001 PHE A 73 TYR 0.019 0.001 TYR C 157 ARG 0.006 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 230 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.7062 (mt) cc_final: 0.6767 (mt) REVERT: B 81 THR cc_start: 0.8772 (p) cc_final: 0.8533 (t) REVERT: B 143 TRP cc_start: 0.8140 (t60) cc_final: 0.7486 (t60) REVERT: B 471 TYR cc_start: 0.8274 (m-80) cc_final: 0.6990 (m-10) REVERT: C 66 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8587 (mm-30) REVERT: C 71 MET cc_start: 0.8416 (mtm) cc_final: 0.8069 (ptp) REVERT: C 75 PHE cc_start: 0.7954 (t80) cc_final: 0.7470 (t80) REVERT: C 172 MET cc_start: 0.7682 (ppp) cc_final: 0.7388 (ppp) REVERT: C 217 ASN cc_start: 0.7780 (m-40) cc_final: 0.7533 (t0) REVERT: C 291 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8826 (mt) REVERT: C 471 TYR cc_start: 0.8320 (m-80) cc_final: 0.6983 (m-10) outliers start: 40 outliers final: 23 residues processed: 253 average time/residue: 0.2180 time to fit residues: 81.8852 Evaluate side-chains 231 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 0.0470 chunk 86 optimal weight: 0.2980 chunk 128 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 36 optimal weight: 5.9990 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 284 GLN A 288 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 GLN B 288 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12027 Z= 0.162 Angle : 0.584 11.292 16338 Z= 0.291 Chirality : 0.040 0.122 1836 Planarity : 0.004 0.042 2031 Dihedral : 4.100 16.722 1557 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.95 % Allowed : 17.06 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1410 helix: 0.78 (0.17), residues: 951 sheet: -1.12 (0.90), residues: 30 loop : -1.76 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 143 HIS 0.004 0.000 HIS C 194 PHE 0.024 0.001 PHE A 73 TYR 0.015 0.001 TYR C 157 ARG 0.003 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 228 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8684 (mtm) cc_final: 0.8208 (ptp) REVERT: A 219 MET cc_start: 0.5058 (ttm) cc_final: 0.4734 (ttt) REVERT: A 310 LEU cc_start: 0.7074 (mt) cc_final: 0.6769 (mt) REVERT: A 365 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6886 (mpp) REVERT: B 81 THR cc_start: 0.8776 (p) cc_final: 0.8499 (t) REVERT: B 422 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7643 (mtp180) REVERT: B 471 TYR cc_start: 0.8275 (m-80) cc_final: 0.6984 (m-10) REVERT: C 62 MET cc_start: 0.7152 (tmm) cc_final: 0.6801 (tmm) REVERT: C 75 PHE cc_start: 0.7724 (t80) cc_final: 0.7299 (t80) REVERT: C 135 ILE cc_start: 0.9099 (mp) cc_final: 0.8618 (tp) REVERT: C 217 ASN cc_start: 0.7706 (m-40) cc_final: 0.7475 (t0) REVERT: C 363 LYS cc_start: 0.7042 (mttt) cc_final: 0.6674 (mtmt) REVERT: C 471 TYR cc_start: 0.8289 (m-80) cc_final: 0.6869 (m-10) outliers start: 50 outliers final: 30 residues processed: 253 average time/residue: 0.2030 time to fit residues: 76.6415 Evaluate side-chains 236 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 0.0020 chunk 122 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 284 GLN C 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12027 Z= 0.189 Angle : 0.616 13.399 16338 Z= 0.304 Chirality : 0.041 0.131 1836 Planarity : 0.004 0.043 2031 Dihedral : 4.128 15.757 1557 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.66 % Allowed : 18.88 % Favored : 76.46 % 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: -0.00 (0.22), residues: 1410 helix: 0.79 (0.17), residues: 951 sheet: None (None), residues: 0 loop : -1.64 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 158 HIS 0.002 0.001 HIS B 54 PHE 0.024 0.001 PHE A 382 TYR 0.015 0.002 TYR B 364 ARG 0.003 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 229 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8706 (mtm) cc_final: 0.8151 (ptp) REVERT: A 219 MET cc_start: 0.5180 (ttm) cc_final: 0.4904 (ttt) REVERT: A 310 LEU cc_start: 0.7096 (mt) cc_final: 0.6771 (mt) REVERT: A 365 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6825 (mpp) REVERT: A 402 LEU cc_start: 0.5829 (mt) cc_final: 0.5232 (mp) REVERT: A 435 GLU cc_start: 0.7324 (tp30) cc_final: 0.6519 (tp30) REVERT: B 72 GLN cc_start: 0.8477 (mt0) cc_final: 0.8175 (mm-40) REVERT: B 164 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7484 (t80) REVERT: B 291 LEU cc_start: 0.9088 (mt) cc_final: 0.8869 (mt) REVERT: B 363 LYS cc_start: 0.7527 (mttt) cc_final: 0.7050 (tttt) REVERT: B 365 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.6602 (mpp) REVERT: B 422 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7663 (mtp180) REVERT: B 471 TYR cc_start: 0.8320 (m-80) cc_final: 0.6965 (m-10) REVERT: B 495 ARG cc_start: 0.7058 (ttm170) cc_final: 0.6602 (ttm170) REVERT: C 71 MET cc_start: 0.8405 (mtm) cc_final: 0.8142 (ptp) REVERT: C 81 THR cc_start: 0.8879 (p) cc_final: 0.8597 (t) REVERT: C 363 LYS cc_start: 0.7039 (mttt) cc_final: 0.6678 (mtmt) REVERT: C 365 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6747 (mpp) REVERT: C 471 TYR cc_start: 0.8373 (m-80) cc_final: 0.7026 (m-10) outliers start: 59 outliers final: 39 residues processed: 261 average time/residue: 0.2045 time to fit residues: 78.5236 Evaluate side-chains 254 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 211 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 448 MET Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12027 Z= 0.178 Angle : 0.604 12.321 16338 Z= 0.300 Chirality : 0.041 0.143 1836 Planarity : 0.004 0.041 2031 Dihedral : 4.083 16.600 1557 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.27 % Allowed : 19.51 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1410 helix: 0.89 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 158 HIS 0.003 0.000 HIS C 194 PHE 0.027 0.001 PHE C 251 TYR 0.016 0.002 TYR A 364 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 232 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8660 (mtm) cc_final: 0.8138 (ptp) REVERT: A 164 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.7035 (t80) REVERT: A 219 MET cc_start: 0.5118 (ttm) cc_final: 0.4854 (ttt) REVERT: A 354 LEU cc_start: 0.8102 (mt) cc_final: 0.7843 (mp) REVERT: A 365 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6823 (mpp) REVERT: A 435 GLU cc_start: 0.7317 (tp30) cc_final: 0.6509 (tp30) REVERT: B 81 THR cc_start: 0.8698 (p) cc_final: 0.8479 (t) REVERT: B 164 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7437 (t80) REVERT: B 291 LEU cc_start: 0.9075 (mt) cc_final: 0.8791 (mt) REVERT: B 363 LYS cc_start: 0.7389 (mttt) cc_final: 0.7048 (tttt) REVERT: B 365 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.6925 (mpp) REVERT: B 422 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7660 (mtp180) REVERT: B 471 TYR cc_start: 0.8423 (m-80) cc_final: 0.7199 (m-10) REVERT: B 495 ARG cc_start: 0.7004 (ttm170) cc_final: 0.6729 (ttm170) REVERT: C 71 MET cc_start: 0.8429 (mtm) cc_final: 0.8082 (ptp) REVERT: C 81 THR cc_start: 0.8901 (p) cc_final: 0.8629 (t) REVERT: C 363 LYS cc_start: 0.7090 (mttt) cc_final: 0.6730 (mtmt) REVERT: C 365 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7261 (mtp) outliers start: 54 outliers final: 38 residues processed: 258 average time/residue: 0.2125 time to fit residues: 80.3397 Evaluate side-chains 255 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 212 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 135 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 84 optimal weight: 0.4980 chunk 54 optimal weight: 20.0000 overall best weight: 1.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12027 Z= 0.193 Angle : 0.626 13.056 16338 Z= 0.309 Chirality : 0.041 0.192 1836 Planarity : 0.004 0.040 2031 Dihedral : 4.125 15.758 1557 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.11 % Allowed : 20.54 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1410 helix: 0.83 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -1.38 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 158 HIS 0.002 0.001 HIS B 54 PHE 0.036 0.001 PHE B 79 TYR 0.017 0.002 TYR B 364 ARG 0.006 0.000 ARG C 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 219 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8683 (mtm) cc_final: 0.8477 (ptm) REVERT: A 164 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6966 (t80) REVERT: A 365 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6996 (mpp) REVERT: A 402 LEU cc_start: 0.5700 (mt) cc_final: 0.5226 (mp) REVERT: A 430 MET cc_start: 0.7059 (ptt) cc_final: 0.6513 (ptt) REVERT: B 81 THR cc_start: 0.8766 (p) cc_final: 0.8534 (t) REVERT: B 164 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7478 (t80) REVERT: B 251 PHE cc_start: 0.7099 (m-10) cc_final: 0.6851 (m-10) REVERT: B 291 LEU cc_start: 0.9096 (mt) cc_final: 0.8795 (mt) REVERT: B 363 LYS cc_start: 0.7403 (mttt) cc_final: 0.7070 (tttt) REVERT: B 365 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.6893 (mpp) REVERT: B 422 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7613 (mtp180) REVERT: B 471 TYR cc_start: 0.8437 (m-80) cc_final: 0.7160 (m-10) REVERT: B 495 ARG cc_start: 0.7109 (ttm170) cc_final: 0.6865 (ttm170) REVERT: C 66 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8857 (mp0) REVERT: C 71 MET cc_start: 0.8439 (mtm) cc_final: 0.8042 (ptp) REVERT: C 81 THR cc_start: 0.8880 (p) cc_final: 0.8582 (t) REVERT: C 330 ARG cc_start: 0.7107 (mtt-85) cc_final: 0.6896 (mtt-85) REVERT: C 363 LYS cc_start: 0.7060 (mttt) cc_final: 0.6742 (ttmt) REVERT: C 365 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6592 (mpp) outliers start: 52 outliers final: 38 residues processed: 245 average time/residue: 0.2072 time to fit residues: 74.4787 Evaluate side-chains 252 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 448 MET Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 106 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12027 Z= 0.179 Angle : 0.627 13.029 16338 Z= 0.308 Chirality : 0.041 0.153 1836 Planarity : 0.004 0.039 2031 Dihedral : 4.094 15.246 1557 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.79 % Allowed : 20.70 % Favored : 75.51 % 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: 0.15 (0.22), residues: 1410 helix: 0.85 (0.17), residues: 939 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 158 HIS 0.003 0.000 HIS A 194 PHE 0.036 0.001 PHE A 382 TYR 0.016 0.002 TYR C 364 ARG 0.009 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 233 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6952 (t80) REVERT: A 310 LEU cc_start: 0.7102 (mt) cc_final: 0.6660 (mt) REVERT: A 365 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.5924 (mpp) REVERT: A 382 PHE cc_start: 0.7737 (t80) cc_final: 0.7461 (t80) REVERT: B 72 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8233 (tp40) REVERT: B 81 THR cc_start: 0.8845 (p) cc_final: 0.8581 (t) REVERT: B 164 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7485 (t80) REVERT: B 172 MET cc_start: 0.7927 (ppp) cc_final: 0.7418 (ppp) REVERT: B 251 PHE cc_start: 0.7092 (m-10) cc_final: 0.6845 (m-10) REVERT: B 330 ARG cc_start: 0.7442 (mtp85) cc_final: 0.7047 (mtp85) REVERT: B 354 LEU cc_start: 0.7974 (mp) cc_final: 0.7388 (tt) REVERT: B 363 LYS cc_start: 0.7403 (mttt) cc_final: 0.7042 (tttt) REVERT: B 365 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.6911 (mpp) REVERT: C 62 MET cc_start: 0.6551 (ttm) cc_final: 0.6187 (tmm) REVERT: C 71 MET cc_start: 0.8479 (mtm) cc_final: 0.8017 (ptp) REVERT: C 81 THR cc_start: 0.8880 (p) cc_final: 0.8604 (t) REVERT: C 363 LYS cc_start: 0.7056 (mttt) cc_final: 0.6738 (ttmt) REVERT: C 365 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6572 (mpp) REVERT: C 471 TYR cc_start: 0.8462 (m-80) cc_final: 0.7304 (m-10) outliers start: 48 outliers final: 33 residues processed: 257 average time/residue: 0.2161 time to fit residues: 81.3011 Evaluate side-chains 256 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 218 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 38 optimal weight: 0.0070 chunk 114 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN C 55 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12027 Z= 0.155 Angle : 0.621 12.609 16338 Z= 0.305 Chirality : 0.041 0.222 1836 Planarity : 0.004 0.053 2031 Dihedral : 4.048 17.508 1557 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.45 % Allowed : 22.20 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1410 helix: 0.91 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.45 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 332 HIS 0.004 0.000 HIS B 210 PHE 0.035 0.001 PHE A 382 TYR 0.016 0.001 TYR A 339 ARG 0.006 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.9050 (ptm) cc_final: 0.8714 (ptp) REVERT: A 164 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7134 (t80) REVERT: A 310 LEU cc_start: 0.7026 (mt) cc_final: 0.6577 (mt) REVERT: A 354 LEU cc_start: 0.7842 (mp) cc_final: 0.7627 (mp) REVERT: A 365 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6503 (mpp) REVERT: B 71 MET cc_start: 0.8754 (mtm) cc_final: 0.8301 (ptp) REVERT: B 81 THR cc_start: 0.8880 (p) cc_final: 0.8603 (t) REVERT: B 164 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7464 (t80) REVERT: B 172 MET cc_start: 0.7858 (ppp) cc_final: 0.7349 (ppp) REVERT: B 251 PHE cc_start: 0.7037 (m-10) cc_final: 0.6795 (m-80) REVERT: B 330 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7091 (mtp85) REVERT: B 354 LEU cc_start: 0.7715 (mp) cc_final: 0.7173 (tt) REVERT: B 363 LYS cc_start: 0.7381 (mttt) cc_final: 0.6991 (tttt) REVERT: B 365 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.6993 (mpp) REVERT: B 448 MET cc_start: 0.6212 (pmm) cc_final: 0.5687 (pmm) REVERT: C 71 MET cc_start: 0.8526 (mtm) cc_final: 0.8098 (ptp) REVERT: C 81 THR cc_start: 0.8879 (p) cc_final: 0.8587 (t) REVERT: C 363 LYS cc_start: 0.7044 (mttt) cc_final: 0.6712 (ttmt) REVERT: C 365 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.6517 (mpp) REVERT: C 428 GLN cc_start: 0.8518 (mp10) cc_final: 0.8309 (mp10) outliers start: 31 outliers final: 21 residues processed: 251 average time/residue: 0.2146 time to fit residues: 78.5968 Evaluate side-chains 244 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12027 Z= 0.164 Angle : 0.640 14.021 16338 Z= 0.314 Chirality : 0.041 0.218 1836 Planarity : 0.004 0.058 2031 Dihedral : 4.006 15.914 1557 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.37 % Allowed : 22.91 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1410 helix: 0.91 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.45 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 143 HIS 0.003 0.000 HIS B 406 PHE 0.040 0.001 PHE A 382 TYR 0.027 0.001 TYR C 157 ARG 0.009 0.000 ARG C 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8960 (ptm) cc_final: 0.8325 (ptp) REVERT: A 164 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7145 (t80) REVERT: A 251 PHE cc_start: 0.6678 (m-10) cc_final: 0.6461 (m-80) REVERT: A 281 GLU cc_start: 0.8971 (pt0) cc_final: 0.8057 (tp30) REVERT: A 310 LEU cc_start: 0.7045 (mt) cc_final: 0.6594 (mt) REVERT: A 354 LEU cc_start: 0.7862 (mp) cc_final: 0.7659 (mp) REVERT: A 365 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6266 (mpp) REVERT: A 382 PHE cc_start: 0.7923 (t80) cc_final: 0.7646 (t80) REVERT: A 430 MET cc_start: 0.6705 (ptt) cc_final: 0.5965 (ptt) REVERT: B 81 THR cc_start: 0.8908 (p) cc_final: 0.8626 (t) REVERT: B 164 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7508 (t80) REVERT: B 251 PHE cc_start: 0.7050 (m-10) cc_final: 0.6808 (m-80) REVERT: B 330 ARG cc_start: 0.7494 (mtp85) cc_final: 0.7174 (mtp85) REVERT: B 354 LEU cc_start: 0.7847 (mp) cc_final: 0.7590 (tt) REVERT: B 363 LYS cc_start: 0.7525 (mttt) cc_final: 0.7115 (tttt) REVERT: B 365 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.6857 (mpp) REVERT: B 448 MET cc_start: 0.6383 (pmm) cc_final: 0.5881 (pmm) REVERT: C 71 MET cc_start: 0.8514 (mtm) cc_final: 0.8104 (ptp) REVERT: C 81 THR cc_start: 0.8842 (p) cc_final: 0.8558 (t) REVERT: C 363 LYS cc_start: 0.7045 (mttt) cc_final: 0.6709 (ttmt) REVERT: C 365 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6493 (mpp) REVERT: C 471 TYR cc_start: 0.8448 (m-80) cc_final: 0.7281 (m-10) outliers start: 30 outliers final: 24 residues processed: 238 average time/residue: 0.2163 time to fit residues: 74.9668 Evaluate side-chains 247 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.0070 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 115 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN B 406 HIS ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.174896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.137825 restraints weight = 17648.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.139171 restraints weight = 9659.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.140568 restraints weight = 7227.198| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12027 Z= 0.156 Angle : 0.666 13.868 16338 Z= 0.323 Chirality : 0.041 0.190 1836 Planarity : 0.004 0.062 2031 Dihedral : 4.007 18.168 1557 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.21 % Allowed : 23.46 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1410 helix: 0.95 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.50 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 143 HIS 0.021 0.001 HIS B 406 PHE 0.041 0.001 PHE A 382 TYR 0.019 0.001 TYR B 339 ARG 0.008 0.000 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.95 seconds wall clock time: 45 minutes 17.95 seconds (2717.95 seconds total)