Starting phenix.real_space_refine on Mon Mar 18 14:59:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/03_2024/7yij_33860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/03_2024/7yij_33860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/03_2024/7yij_33860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/03_2024/7yij_33860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/03_2024/7yij_33860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/03_2024/7yij_33860.pdb" } resolution = 3.8 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= 0.001 sd= 0.029 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: 5 Type Number sf(0) Gaussians K 1 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C GLU 582": "OE1" <-> "OE2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 503": "OE1" <-> "OE2" Residue "D GLU 582": "OE1" <-> "OE2" Residue "D GLU 596": "OE1" <-> "OE2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21313 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.94, per 1000 atoms: 0.51 Number of scatterers: 21313 At special positions: 0 Unit cell: (146.877, 146.877, 129.897, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 1 19.00 S 128 16.00 O 3844 8.00 N 3544 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 4.0 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 43.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.598A pdb=" N GLU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 4.142A pdb=" N THR A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.500A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 245 through 265 removed outlier: 3.523A pdb=" N VAL A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 300 removed outlier: 3.959A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.561A pdb=" N LYS A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 375 removed outlier: 4.061A pdb=" N VAL A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 3.608A pdb=" N GLN A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 442 through 463 removed outlier: 3.860A pdb=" N LYS A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.170A pdb=" N THR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.847A pdb=" N SER A 502 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.790A pdb=" N ILE A 527 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 528 " --> pdb=" O LEU A 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 524 through 528' Processing helix chain 'A' and resid 529 through 542 removed outlier: 3.895A pdb=" N ASN A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 643 through 653 removed outlier: 3.961A pdb=" N LYS A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.799A pdb=" N ASN A 658 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.715A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.598A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 4.142A pdb=" N THR B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.500A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.523A pdb=" N VAL B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 300 removed outlier: 3.959A pdb=" N PHE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 327 through 330 Processing helix chain 'B' and resid 331 through 337 removed outlier: 3.561A pdb=" N LYS B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 375 removed outlier: 4.061A pdb=" N VAL B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 removed outlier: 3.608A pdb=" N GLN B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 442 through 463 removed outlier: 3.860A pdb=" N LYS B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 494 removed outlier: 4.171A pdb=" N THR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 removed outlier: 3.847A pdb=" N SER B 502 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 removed outlier: 3.790A pdb=" N ILE B 527 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS B 528 " --> pdb=" O LEU B 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 528' Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.895A pdb=" N ASN B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 Processing helix chain 'B' and resid 643 through 653 removed outlier: 3.961A pdb=" N LYS B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 649 " --> pdb=" O ALA B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.799A pdb=" N ASN B 658 " --> pdb=" O ALA B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 691 removed outlier: 3.715A pdb=" N ARG B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.598A pdb=" N GLU C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 4.142A pdb=" N THR C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.500A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 245 through 265 removed outlier: 3.523A pdb=" N VAL C 249 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 300 removed outlier: 3.959A pdb=" N PHE C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 327 through 330 Processing helix chain 'C' and resid 331 through 337 removed outlier: 3.561A pdb=" N LYS C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 375 removed outlier: 4.061A pdb=" N VAL C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 397 removed outlier: 3.608A pdb=" N GLN C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 442 through 463 removed outlier: 3.860A pdb=" N LYS C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 494 removed outlier: 4.171A pdb=" N THR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 514 removed outlier: 3.847A pdb=" N SER C 502 " --> pdb=" O PRO C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.790A pdb=" N ILE C 527 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS C 528 " --> pdb=" O LEU C 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 524 through 528' Processing helix chain 'C' and resid 529 through 542 removed outlier: 3.895A pdb=" N ASN C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 Processing helix chain 'C' and resid 643 through 653 removed outlier: 3.961A pdb=" N LYS C 648 " --> pdb=" O GLU C 644 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL C 649 " --> pdb=" O ALA C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 658 removed outlier: 3.799A pdb=" N ASN C 658 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 691 removed outlier: 3.715A pdb=" N ARG C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.597A pdb=" N GLU D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 154 removed outlier: 4.142A pdb=" N THR D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.500A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 245 through 265 removed outlier: 3.523A pdb=" N VAL D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP D 251 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 300 removed outlier: 3.959A pdb=" N PHE D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 327 through 330 Processing helix chain 'D' and resid 331 through 337 removed outlier: 3.561A pdb=" N LYS D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 375 removed outlier: 4.061A pdb=" N VAL D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 397 removed outlier: 3.608A pdb=" N GLN D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 442 through 463 removed outlier: 3.860A pdb=" N LYS D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 494 removed outlier: 4.171A pdb=" N THR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 514 removed outlier: 3.847A pdb=" N SER D 502 " --> pdb=" O PRO D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 528 removed outlier: 3.790A pdb=" N ILE D 527 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS D 528 " --> pdb=" O LEU D 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 528' Processing helix chain 'D' and resid 529 through 542 removed outlier: 3.895A pdb=" N ASN D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG D 542 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 Processing helix chain 'D' and resid 643 through 653 removed outlier: 3.961A pdb=" N LYS D 648 " --> pdb=" O GLU D 644 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 658 removed outlier: 3.799A pdb=" N ASN D 658 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 691 removed outlier: 3.715A pdb=" N ARG D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 567 through 570 removed outlier: 6.770A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 641 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 587 " --> pdb=" O ILE A 641 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 603 through 606 removed outlier: 4.108A pdb=" N ALA A 605 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 567 through 570 removed outlier: 6.770A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 641 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 587 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 603 through 606 removed outlier: 4.108A pdb=" N ALA B 605 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 567 through 570 removed outlier: 6.770A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 641 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 587 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 603 through 606 removed outlier: 4.108A pdb=" N ALA C 605 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 567 through 570 removed outlier: 6.770A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 641 " --> pdb=" O LEU D 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 587 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 603 through 606 removed outlier: 4.108A pdb=" N ALA D 605 " --> pdb=" O VAL D 597 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 8.46 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: 6668 1.34 - 1.46: 5264 1.46 - 1.58: 9680 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" CA ASP C 37 " pdb=" C ASP C 37 " ideal model delta sigma weight residual 1.519 1.544 -0.025 1.01e-02 9.80e+03 6.04e+00 bond pdb=" CA ASP B 37 " pdb=" C ASP B 37 " ideal model delta sigma weight residual 1.519 1.544 -0.025 1.01e-02 9.80e+03 6.04e+00 bond pdb=" CA ASP D 37 " pdb=" C ASP D 37 " ideal model delta sigma weight residual 1.519 1.544 -0.025 1.01e-02 9.80e+03 6.04e+00 bond pdb=" CA ASP A 37 " pdb=" C ASP A 37 " ideal model delta sigma weight residual 1.519 1.544 -0.025 1.01e-02 9.80e+03 6.04e+00 bond pdb=" CB THR B 468 " pdb=" CG2 THR B 468 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.59e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.35: 500 106.35 - 113.69: 12277 113.69 - 121.03: 10571 121.03 - 128.38: 6048 128.38 - 135.72: 188 Bond angle restraints: 29584 Sorted by residual: angle pdb=" CA TRP C 38 " pdb=" CB TRP C 38 " pdb=" CG TRP C 38 " ideal model delta sigma weight residual 113.60 125.80 -12.20 1.90e+00 2.77e-01 4.12e+01 angle pdb=" CA TRP D 38 " pdb=" CB TRP D 38 " pdb=" CG TRP D 38 " ideal model delta sigma weight residual 113.60 125.80 -12.20 1.90e+00 2.77e-01 4.12e+01 angle pdb=" CA TRP A 38 " pdb=" CB TRP A 38 " pdb=" CG TRP A 38 " ideal model delta sigma weight residual 113.60 125.80 -12.20 1.90e+00 2.77e-01 4.12e+01 angle pdb=" CA TRP B 38 " pdb=" CB TRP B 38 " pdb=" CG TRP B 38 " ideal model delta sigma weight residual 113.60 125.80 -12.20 1.90e+00 2.77e-01 4.12e+01 angle pdb=" C GLU B 378 " pdb=" N VAL B 379 " pdb=" CA VAL B 379 " ideal model delta sigma weight residual 121.97 132.45 -10.48 1.80e+00 3.09e-01 3.39e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 11310 16.36 - 32.72: 1318 32.72 - 49.08: 244 49.08 - 65.43: 36 65.43 - 81.79: 24 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA GLN B 34 " pdb=" C GLN B 34 " pdb=" N ILE B 35 " pdb=" CA ILE B 35 " ideal model delta harmonic sigma weight residual -180.00 -133.57 -46.43 0 5.00e+00 4.00e-02 8.62e+01 dihedral pdb=" CA GLN D 34 " pdb=" C GLN D 34 " pdb=" N ILE D 35 " pdb=" CA ILE D 35 " ideal model delta harmonic sigma weight residual 180.00 -133.57 -46.43 0 5.00e+00 4.00e-02 8.62e+01 dihedral pdb=" CA GLN A 34 " pdb=" C GLN A 34 " pdb=" N ILE A 35 " pdb=" CA ILE A 35 " ideal model delta harmonic sigma weight residual -180.00 -133.57 -46.43 0 5.00e+00 4.00e-02 8.62e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3144 0.089 - 0.177: 212 0.177 - 0.266: 40 0.266 - 0.355: 4 0.355 - 0.443: 4 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CB THR D 468 " pdb=" CA THR D 468 " pdb=" OG1 THR D 468 " pdb=" CG2 THR D 468 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CB THR A 468 " pdb=" CA THR A 468 " pdb=" OG1 THR A 468 " pdb=" CG2 THR A 468 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CB THR B 468 " pdb=" CA THR B 468 " pdb=" OG1 THR B 468 " pdb=" CG2 THR B 468 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 676 " 0.031 2.00e-02 2.50e+03 3.32e-02 1.92e+01 pdb=" CG PHE B 676 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE B 676 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 676 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 676 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 676 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 676 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 676 " -0.031 2.00e-02 2.50e+03 3.32e-02 1.92e+01 pdb=" CG PHE C 676 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE C 676 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE C 676 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 676 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 676 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 676 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 676 " -0.031 2.00e-02 2.50e+03 3.31e-02 1.92e+01 pdb=" CG PHE D 676 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE D 676 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE D 676 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 676 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 676 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE D 676 " -0.001 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.74: 1803 2.74 - 3.34: 25854 3.34 - 3.94: 39922 3.94 - 4.54: 51246 4.54 - 5.14: 78234 Nonbonded interactions: 197059 Sorted by model distance: nonbonded pdb=" O GLY A 465 " pdb=" OG1 THR A 468 " model vdw 2.135 2.440 nonbonded pdb=" O GLY D 465 " pdb=" OG1 THR D 468 " model vdw 2.136 2.440 nonbonded pdb=" O GLY C 465 " pdb=" OG1 THR C 468 " model vdw 2.136 2.440 nonbonded pdb=" O GLY B 465 " pdb=" OG1 THR B 468 " model vdw 2.136 2.440 nonbonded pdb=" O THR D 512 " pdb=" OG SER D 516 " model vdw 2.144 2.440 ... (remaining 197054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 692) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.770 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: 14.230 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 54.190 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 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 : 0.004 0.078 21804 Z= 0.284 Angle : 0.925 13.920 29584 Z= 0.526 Chirality : 0.054 0.443 3404 Planarity : 0.006 0.068 3668 Dihedral : 14.448 81.792 7884 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 1.38 % Allowed : 13.30 % Favored : 85.32 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.16), residues: 2616 helix: 0.10 (0.16), residues: 1076 sheet: -1.98 (0.58), residues: 88 loop : -3.50 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 38 HIS 0.008 0.001 HIS D 539 PHE 0.076 0.002 PHE C 676 TYR 0.038 0.002 TYR C 195 ARG 0.008 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.463 Fit side-chains REVERT: A 376 ILE cc_start: 0.5143 (tt) cc_final: 0.4833 (mt) REVERT: A 442 THR cc_start: 0.8832 (p) cc_final: 0.8562 (t) REVERT: A 513 TRP cc_start: 0.7390 (m-10) cc_final: 0.7139 (m-10) REVERT: A 647 LEU cc_start: 0.8750 (pp) cc_final: 0.8478 (mt) REVERT: A 658 ASN cc_start: 0.6591 (t0) cc_final: 0.6361 (t0) REVERT: B 376 ILE cc_start: 0.5114 (tt) cc_final: 0.4811 (mt) REVERT: B 442 THR cc_start: 0.8738 (p) cc_final: 0.8502 (t) REVERT: B 513 TRP cc_start: 0.7396 (m-10) cc_final: 0.7142 (m-10) REVERT: B 647 LEU cc_start: 0.8739 (pp) cc_final: 0.8471 (mt) REVERT: B 658 ASN cc_start: 0.6599 (t0) cc_final: 0.6369 (t0) REVERT: C 376 ILE cc_start: 0.5141 (tt) cc_final: 0.4840 (mt) REVERT: C 442 THR cc_start: 0.8724 (p) cc_final: 0.8456 (t) REVERT: C 513 TRP cc_start: 0.7408 (m-10) cc_final: 0.7154 (m-10) REVERT: C 647 LEU cc_start: 0.8739 (pp) cc_final: 0.8472 (mt) REVERT: C 658 ASN cc_start: 0.6583 (t0) cc_final: 0.6350 (t0) REVERT: D 376 ILE cc_start: 0.5168 (tt) cc_final: 0.4858 (mt) REVERT: D 442 THR cc_start: 0.8746 (p) cc_final: 0.8472 (t) REVERT: D 513 TRP cc_start: 0.7407 (m-10) cc_final: 0.7152 (m-10) REVERT: D 647 LEU cc_start: 0.8752 (pp) cc_final: 0.8482 (mt) REVERT: D 658 ASN cc_start: 0.6579 (t0) cc_final: 0.6347 (t0) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2780 time to fit residues: 145.2566 Evaluate side-chains 240 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.7980 chunk 200 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 21804 Z= 0.217 Angle : 0.765 18.827 29584 Z= 0.406 Chirality : 0.047 0.279 3404 Planarity : 0.005 0.054 3668 Dihedral : 6.310 47.159 2864 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 1.38 % Allowed : 12.84 % Favored : 85.78 % Rotamer: Outliers : 1.68 % Allowed : 9.58 % Favored : 88.74 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.16), residues: 2616 helix: 0.25 (0.16), residues: 1136 sheet: -1.61 (0.61), residues: 88 loop : -3.35 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 38 HIS 0.006 0.001 HIS A 539 PHE 0.051 0.002 PHE C 676 TYR 0.013 0.001 TYR D 508 ARG 0.010 0.001 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 273 time to evaluate : 2.593 Fit side-chains REVERT: A 109 MET cc_start: 0.2119 (pmm) cc_final: 0.1617 (pmm) REVERT: A 506 MET cc_start: 0.8143 (tmm) cc_final: 0.7853 (tmm) REVERT: A 509 ILE cc_start: 0.8973 (pt) cc_final: 0.8753 (mm) REVERT: A 513 TRP cc_start: 0.7524 (m-10) cc_final: 0.7003 (m-10) REVERT: A 658 ASN cc_start: 0.6614 (t0) cc_final: 0.6400 (t0) REVERT: B 109 MET cc_start: 0.2088 (pmm) cc_final: 0.1589 (pmm) REVERT: B 506 MET cc_start: 0.8127 (tmm) cc_final: 0.7838 (tmm) REVERT: B 509 ILE cc_start: 0.8981 (pt) cc_final: 0.8764 (mm) REVERT: B 513 TRP cc_start: 0.7529 (m-10) cc_final: 0.7006 (m-10) REVERT: B 658 ASN cc_start: 0.6626 (t0) cc_final: 0.6409 (t0) REVERT: C 109 MET cc_start: 0.2067 (pmm) cc_final: 0.1567 (pmm) REVERT: C 506 MET cc_start: 0.8144 (tmm) cc_final: 0.7855 (tmm) REVERT: C 509 ILE cc_start: 0.8979 (pt) cc_final: 0.8763 (mm) REVERT: C 513 TRP cc_start: 0.7542 (m-10) cc_final: 0.7017 (m-10) REVERT: C 658 ASN cc_start: 0.6608 (t0) cc_final: 0.6392 (t0) REVERT: D 109 MET cc_start: 0.2102 (pmm) cc_final: 0.1601 (pmm) REVERT: D 506 MET cc_start: 0.8153 (tmm) cc_final: 0.7864 (tmm) REVERT: D 509 ILE cc_start: 0.8977 (pt) cc_final: 0.8760 (mm) REVERT: D 513 TRP cc_start: 0.7540 (m-10) cc_final: 0.7011 (m-10) REVERT: D 658 ASN cc_start: 0.6594 (t0) cc_final: 0.6378 (t0) outliers start: 40 outliers final: 36 residues processed: 305 average time/residue: 0.2869 time to fit residues: 141.6376 Evaluate side-chains 271 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 235 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 38 TRP Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain D residue 38 TRP Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 564 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.0870 chunk 74 optimal weight: 9.9990 chunk 199 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 0.9980 chunk 259 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 chunk 81 optimal weight: 0.0870 chunk 192 optimal weight: 0.8980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 477 ASN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 477 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 21804 Z= 0.202 Angle : 0.731 19.503 29584 Z= 0.385 Chirality : 0.045 0.245 3404 Planarity : 0.004 0.055 3668 Dihedral : 5.963 49.595 2864 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.15 % Favored : 85.63 % Rotamer: Outliers : 2.02 % Allowed : 14.37 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.17), residues: 2616 helix: 0.55 (0.16), residues: 1136 sheet: -1.58 (0.60), residues: 88 loop : -3.22 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 618 HIS 0.005 0.001 HIS A 539 PHE 0.039 0.002 PHE B 676 TYR 0.011 0.001 TYR A 69 ARG 0.004 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 265 time to evaluate : 2.510 Fit side-chains REVERT: A 270 PHE cc_start: 0.7244 (t80) cc_final: 0.6978 (t80) REVERT: A 506 MET cc_start: 0.8147 (tmm) cc_final: 0.7866 (tmm) REVERT: A 513 TRP cc_start: 0.7529 (m-10) cc_final: 0.7022 (m-10) REVERT: A 560 ARG cc_start: 0.7807 (mtm180) cc_final: 0.6804 (mmt90) REVERT: A 676 PHE cc_start: 0.4402 (OUTLIER) cc_final: 0.3112 (p90) REVERT: B 270 PHE cc_start: 0.7257 (t80) cc_final: 0.6996 (t80) REVERT: B 506 MET cc_start: 0.8133 (tmm) cc_final: 0.7853 (tmm) REVERT: B 513 TRP cc_start: 0.7534 (m-10) cc_final: 0.7023 (m-10) REVERT: B 560 ARG cc_start: 0.7796 (mtm180) cc_final: 0.6797 (mmt90) REVERT: B 676 PHE cc_start: 0.4399 (OUTLIER) cc_final: 0.3111 (p90) REVERT: C 506 MET cc_start: 0.8147 (tmm) cc_final: 0.7867 (tmm) REVERT: C 513 TRP cc_start: 0.7544 (m-10) cc_final: 0.7037 (m-10) REVERT: C 560 ARG cc_start: 0.7814 (mtm180) cc_final: 0.6805 (mmt90) REVERT: C 676 PHE cc_start: 0.4398 (OUTLIER) cc_final: 0.3106 (p90) REVERT: D 270 PHE cc_start: 0.7251 (t80) cc_final: 0.6985 (t80) REVERT: D 506 MET cc_start: 0.8162 (tmm) cc_final: 0.7877 (tmm) REVERT: D 513 TRP cc_start: 0.7544 (m-10) cc_final: 0.7033 (m-10) REVERT: D 560 ARG cc_start: 0.7811 (mtm180) cc_final: 0.6804 (mmt90) REVERT: D 676 PHE cc_start: 0.4405 (OUTLIER) cc_final: 0.3113 (p90) outliers start: 48 outliers final: 36 residues processed: 293 average time/residue: 0.2700 time to fit residues: 129.8511 Evaluate side-chains 283 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 243 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 676 PHE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 114 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 255 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 21804 Z= 0.229 Angle : 0.735 19.609 29584 Z= 0.387 Chirality : 0.046 0.260 3404 Planarity : 0.004 0.056 3668 Dihedral : 5.886 48.104 2864 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 1.38 % Allowed : 12.54 % Favored : 86.09 % Rotamer: Outliers : 3.32 % Allowed : 15.92 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.99 (0.17), residues: 2616 helix: 0.65 (0.16), residues: 1128 sheet: -1.86 (0.59), residues: 88 loop : -3.17 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 618 HIS 0.006 0.001 HIS A 539 PHE 0.039 0.002 PHE B 676 TYR 0.015 0.001 TYR D 419 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 278 time to evaluate : 2.504 Fit side-chains REVERT: A 109 MET cc_start: 0.2460 (pmm) cc_final: 0.2085 (pmm) REVERT: A 270 PHE cc_start: 0.7347 (t80) cc_final: 0.7084 (t80) REVERT: A 513 TRP cc_start: 0.7419 (m-10) cc_final: 0.7095 (m-10) REVERT: A 560 ARG cc_start: 0.7807 (mtm180) cc_final: 0.6836 (mmt90) REVERT: B 109 MET cc_start: 0.2423 (pmm) cc_final: 0.2046 (pmm) REVERT: B 270 PHE cc_start: 0.7357 (t80) cc_final: 0.7098 (t80) REVERT: B 513 TRP cc_start: 0.7426 (m-10) cc_final: 0.7098 (m-10) REVERT: B 560 ARG cc_start: 0.7803 (mtm180) cc_final: 0.6834 (mmt90) REVERT: C 109 MET cc_start: 0.2399 (pmm) cc_final: 0.2027 (pmm) REVERT: C 513 TRP cc_start: 0.7432 (m-10) cc_final: 0.7113 (m-10) REVERT: C 560 ARG cc_start: 0.7850 (mtm180) cc_final: 0.6869 (mmt90) REVERT: D 109 MET cc_start: 0.2426 (pmm) cc_final: 0.2060 (pmm) REVERT: D 270 PHE cc_start: 0.7354 (t80) cc_final: 0.7094 (t80) REVERT: D 513 TRP cc_start: 0.7432 (m-10) cc_final: 0.7105 (m-10) REVERT: D 560 ARG cc_start: 0.7812 (mtm180) cc_final: 0.6839 (mmt90) outliers start: 79 outliers final: 52 residues processed: 325 average time/residue: 0.2724 time to fit residues: 146.3885 Evaluate side-chains 315 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 263 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.0270 chunk 144 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 229 optimal weight: 0.0970 chunk 64 optimal weight: 7.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 21804 Z= 0.309 Angle : 0.797 19.234 29584 Z= 0.418 Chirality : 0.049 0.244 3404 Planarity : 0.005 0.056 3668 Dihedral : 6.130 47.154 2864 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 1.38 % Allowed : 14.49 % Favored : 84.14 % Rotamer: Outliers : 4.03 % Allowed : 17.94 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.17), residues: 2616 helix: 0.22 (0.15), residues: 1164 sheet: -2.22 (0.56), residues: 88 loop : -3.13 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 618 HIS 0.009 0.001 HIS A 539 PHE 0.047 0.003 PHE C 676 TYR 0.018 0.002 TYR B 419 ARG 0.005 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 283 time to evaluate : 2.257 Fit side-chains REVERT: A 270 PHE cc_start: 0.7439 (t80) cc_final: 0.7195 (t80) REVERT: A 447 MET cc_start: 0.8658 (mtm) cc_final: 0.8405 (mtm) REVERT: A 513 TRP cc_start: 0.7479 (m-10) cc_final: 0.7110 (m-10) REVERT: A 532 MET cc_start: 0.5347 (ppp) cc_final: 0.4990 (ppp) REVERT: B 270 PHE cc_start: 0.7448 (t80) cc_final: 0.7208 (t80) REVERT: B 513 TRP cc_start: 0.7485 (m-10) cc_final: 0.7112 (m-10) REVERT: B 532 MET cc_start: 0.5350 (ppp) cc_final: 0.4990 (ppp) REVERT: C 447 MET cc_start: 0.8607 (mtm) cc_final: 0.8397 (mtm) REVERT: C 513 TRP cc_start: 0.7491 (m-10) cc_final: 0.7120 (m-10) REVERT: C 532 MET cc_start: 0.5352 (ppp) cc_final: 0.4990 (ppp) REVERT: D 270 PHE cc_start: 0.7444 (t80) cc_final: 0.7201 (t80) REVERT: D 447 MET cc_start: 0.8642 (mtm) cc_final: 0.8396 (mtm) REVERT: D 513 TRP cc_start: 0.7490 (m-10) cc_final: 0.7119 (m-10) REVERT: D 532 MET cc_start: 0.5355 (ppp) cc_final: 0.4996 (ppp) outliers start: 96 outliers final: 60 residues processed: 347 average time/residue: 0.2806 time to fit residues: 158.3260 Evaluate side-chains 326 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 266 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 255 optimal weight: 0.9990 chunk 212 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 21804 Z= 0.309 Angle : 0.776 18.086 29584 Z= 0.411 Chirality : 0.048 0.263 3404 Planarity : 0.005 0.056 3668 Dihedral : 5.992 44.962 2864 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 1.38 % Allowed : 13.46 % Favored : 85.17 % Rotamer: Outliers : 4.83 % Allowed : 19.45 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.17), residues: 2616 helix: 0.25 (0.16), residues: 1140 sheet: -2.28 (0.57), residues: 88 loop : -3.08 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 618 HIS 0.005 0.001 HIS C 539 PHE 0.034 0.002 PHE B 491 TYR 0.015 0.002 TYR B 419 ARG 0.004 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 300 time to evaluate : 2.543 Fit side-chains REVERT: A 107 PHE cc_start: -0.1622 (OUTLIER) cc_final: -0.2209 (m-80) REVERT: A 109 MET cc_start: 0.2850 (pmm) cc_final: -0.0829 (ptt) REVERT: A 341 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7825 (p90) REVERT: A 513 TRP cc_start: 0.7543 (m-10) cc_final: 0.7163 (m-10) REVERT: A 522 GLU cc_start: 0.7776 (mm-30) cc_final: 0.6655 (pm20) REVERT: B 107 PHE cc_start: -0.1594 (OUTLIER) cc_final: -0.2189 (m-80) REVERT: B 109 MET cc_start: 0.2818 (pmm) cc_final: -0.0851 (ptt) REVERT: B 341 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7813 (p90) REVERT: B 513 TRP cc_start: 0.7549 (m-10) cc_final: 0.7170 (m-10) REVERT: B 522 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6656 (pm20) REVERT: C 107 PHE cc_start: -0.1593 (OUTLIER) cc_final: -0.2189 (m-80) REVERT: C 109 MET cc_start: 0.2803 (pmm) cc_final: -0.0891 (ptt) REVERT: C 207 ILE cc_start: 0.8755 (mp) cc_final: 0.8543 (mm) REVERT: C 341 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7814 (p90) REVERT: C 513 TRP cc_start: 0.7559 (m-10) cc_final: 0.7178 (m-10) REVERT: C 522 GLU cc_start: 0.7721 (mm-30) cc_final: 0.6622 (pm20) REVERT: D 107 PHE cc_start: -0.1616 (OUTLIER) cc_final: -0.2213 (m-80) REVERT: D 109 MET cc_start: 0.2833 (pmm) cc_final: -0.0863 (ptt) REVERT: D 341 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7821 (p90) REVERT: D 513 TRP cc_start: 0.7557 (m-10) cc_final: 0.7171 (m-10) REVERT: D 522 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6617 (pm20) outliers start: 115 outliers final: 67 residues processed: 371 average time/residue: 0.2858 time to fit residues: 171.0631 Evaluate side-chains 347 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 272 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 254 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21804 Z= 0.357 Angle : 0.830 18.382 29584 Z= 0.437 Chirality : 0.050 0.300 3404 Planarity : 0.005 0.056 3668 Dihedral : 6.199 43.133 2864 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 1.22 % Allowed : 15.06 % Favored : 83.72 % Rotamer: Outliers : 5.08 % Allowed : 20.84 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 2616 helix: 0.15 (0.16), residues: 1140 sheet: -2.32 (0.55), residues: 88 loop : -3.16 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 618 HIS 0.005 0.001 HIS C 539 PHE 0.035 0.003 PHE C 491 TYR 0.015 0.002 TYR B 419 ARG 0.006 0.000 ARG B 533 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 282 time to evaluate : 2.414 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 58 VAL cc_start: 0.0703 (OUTLIER) cc_final: 0.0430 (p) REVERT: A 107 PHE cc_start: -0.0938 (OUTLIER) cc_final: -0.1795 (m-80) REVERT: A 109 MET cc_start: 0.2608 (pmm) cc_final: -0.0662 (ptt) REVERT: A 207 ILE cc_start: 0.8809 (mp) cc_final: 0.8454 (mm) REVERT: A 341 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7879 (p90) REVERT: A 447 MET cc_start: 0.8748 (mtm) cc_final: 0.8422 (mtm) REVERT: A 513 TRP cc_start: 0.7543 (m-10) cc_final: 0.7146 (m-10) REVERT: A 522 GLU cc_start: 0.7809 (mm-30) cc_final: 0.6810 (pm20) REVERT: B 58 VAL cc_start: 0.0683 (OUTLIER) cc_final: 0.0407 (p) REVERT: B 107 PHE cc_start: -0.0917 (OUTLIER) cc_final: -0.1782 (m-80) REVERT: B 109 MET cc_start: 0.2552 (pmm) cc_final: -0.0703 (ptt) REVERT: B 207 ILE cc_start: 0.8796 (mp) cc_final: 0.8442 (mm) REVERT: B 341 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7885 (p90) REVERT: B 513 TRP cc_start: 0.7584 (m-10) cc_final: 0.7167 (m-10) REVERT: B 522 GLU cc_start: 0.7817 (mm-30) cc_final: 0.6810 (pm20) REVERT: C 58 VAL cc_start: 0.0698 (OUTLIER) cc_final: 0.0424 (p) REVERT: C 107 PHE cc_start: -0.0907 (OUTLIER) cc_final: -0.1785 (m-80) REVERT: C 109 MET cc_start: 0.2564 (pmm) cc_final: -0.0717 (ptt) REVERT: C 207 ILE cc_start: 0.8814 (mp) cc_final: 0.8557 (mm) REVERT: C 341 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7865 (p90) REVERT: C 447 MET cc_start: 0.8701 (mtm) cc_final: 0.8420 (mtm) REVERT: C 513 TRP cc_start: 0.7590 (m-10) cc_final: 0.7177 (m-10) REVERT: C 522 GLU cc_start: 0.7787 (mm-30) cc_final: 0.6816 (pm20) REVERT: D 58 VAL cc_start: 0.0706 (OUTLIER) cc_final: 0.0434 (p) REVERT: D 107 PHE cc_start: -0.0937 (OUTLIER) cc_final: -0.1803 (m-80) REVERT: D 109 MET cc_start: 0.2587 (pmm) cc_final: -0.0706 (ptt) REVERT: D 207 ILE cc_start: 0.8790 (mp) cc_final: 0.8431 (mm) REVERT: D 341 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7871 (p90) REVERT: D 447 MET cc_start: 0.8737 (mtm) cc_final: 0.8419 (mtm) REVERT: D 513 TRP cc_start: 0.7581 (m-10) cc_final: 0.7177 (m-10) REVERT: D 522 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6810 (pm20) outliers start: 121 outliers final: 63 residues processed: 366 average time/residue: 0.2970 time to fit residues: 180.0057 Evaluate side-chains 332 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 257 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 151 optimal weight: 0.2980 chunk 76 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 231 optimal weight: 0.5980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 473 GLN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 473 GLN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS C 473 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS D 473 GLN ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21804 Z= 0.195 Angle : 0.727 18.397 29584 Z= 0.383 Chirality : 0.045 0.233 3404 Planarity : 0.004 0.057 3668 Dihedral : 5.720 41.999 2864 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 1.22 % Allowed : 12.58 % Favored : 86.20 % Rotamer: Outliers : 3.40 % Allowed : 22.44 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2616 helix: 0.42 (0.16), residues: 1148 sheet: -2.47 (0.55), residues: 88 loop : -3.10 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 618 HIS 0.021 0.001 HIS C 482 PHE 0.024 0.002 PHE A 491 TYR 0.015 0.001 TYR C 508 ARG 0.003 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 293 time to evaluate : 2.429 Fit side-chains REVERT: A 58 VAL cc_start: 0.0592 (OUTLIER) cc_final: 0.0386 (p) REVERT: A 76 LYS cc_start: 0.7567 (tptt) cc_final: 0.7042 (tptt) REVERT: A 107 PHE cc_start: -0.0914 (OUTLIER) cc_final: -0.1781 (m-80) REVERT: A 109 MET cc_start: 0.2549 (pmm) cc_final: -0.1141 (ptt) REVERT: A 207 ILE cc_start: 0.8704 (mp) cc_final: 0.8350 (mm) REVERT: A 447 MET cc_start: 0.8709 (mtm) cc_final: 0.8261 (mtm) REVERT: A 513 TRP cc_start: 0.7467 (m-10) cc_final: 0.7126 (m-10) REVERT: A 522 GLU cc_start: 0.7715 (mm-30) cc_final: 0.6749 (pm20) REVERT: A 533 ARG cc_start: 0.7710 (tmm-80) cc_final: 0.7507 (ttp-110) REVERT: B 58 VAL cc_start: 0.0568 (OUTLIER) cc_final: 0.0363 (p) REVERT: B 76 LYS cc_start: 0.7572 (tptt) cc_final: 0.7045 (tptt) REVERT: B 107 PHE cc_start: -0.0900 (OUTLIER) cc_final: -0.1767 (m-80) REVERT: B 109 MET cc_start: 0.2504 (pmm) cc_final: -0.1179 (ptt) REVERT: B 207 ILE cc_start: 0.8690 (mp) cc_final: 0.8334 (mm) REVERT: B 513 TRP cc_start: 0.7473 (m-10) cc_final: 0.7123 (m-10) REVERT: B 522 GLU cc_start: 0.7715 (mm-30) cc_final: 0.6747 (pm20) REVERT: B 533 ARG cc_start: 0.7711 (tmm-80) cc_final: 0.7498 (ttp-110) REVERT: C 58 VAL cc_start: 0.0585 (OUTLIER) cc_final: 0.0378 (p) REVERT: C 76 LYS cc_start: 0.7558 (tptt) cc_final: 0.7037 (tptt) REVERT: C 107 PHE cc_start: -0.0884 (OUTLIER) cc_final: -0.1768 (m-80) REVERT: C 109 MET cc_start: 0.2504 (pmm) cc_final: -0.1203 (ptt) REVERT: C 207 ILE cc_start: 0.8658 (mp) cc_final: 0.8354 (mm) REVERT: C 447 MET cc_start: 0.8656 (mtm) cc_final: 0.8258 (mtm) REVERT: C 513 TRP cc_start: 0.7483 (m-10) cc_final: 0.7105 (m-10) REVERT: C 522 GLU cc_start: 0.7778 (mm-30) cc_final: 0.6808 (pm20) REVERT: D 58 VAL cc_start: 0.0588 (OUTLIER) cc_final: 0.0385 (p) REVERT: D 76 LYS cc_start: 0.7541 (tptt) cc_final: 0.7024 (tptt) REVERT: D 107 PHE cc_start: -0.0903 (OUTLIER) cc_final: -0.1782 (m-80) REVERT: D 109 MET cc_start: 0.2526 (pmm) cc_final: -0.1186 (ptt) REVERT: D 207 ILE cc_start: 0.8679 (mp) cc_final: 0.8319 (mm) REVERT: D 447 MET cc_start: 0.8692 (mtm) cc_final: 0.8254 (mtm) REVERT: D 513 TRP cc_start: 0.7482 (m-10) cc_final: 0.7144 (m-10) REVERT: D 522 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6801 (pm20) outliers start: 81 outliers final: 40 residues processed: 350 average time/residue: 0.2715 time to fit residues: 155.6351 Evaluate side-chains 318 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 270 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 chunk 224 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS A 473 GLN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 473 GLN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS C 473 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS D 473 GLN ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21804 Z= 0.281 Angle : 0.773 17.727 29584 Z= 0.406 Chirality : 0.047 0.219 3404 Planarity : 0.005 0.081 3668 Dihedral : 5.769 40.400 2864 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 1.22 % Allowed : 15.21 % Favored : 83.56 % Rotamer: Outliers : 3.78 % Allowed : 23.15 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.17), residues: 2616 helix: 0.25 (0.16), residues: 1164 sheet: -2.49 (0.54), residues: 88 loop : -3.19 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 618 HIS 0.004 0.001 HIS C 539 PHE 0.029 0.002 PHE D 491 TYR 0.019 0.002 TYR C 419 ARG 0.011 0.000 ARG D 533 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 273 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: -0.0688 (OUTLIER) cc_final: -0.1638 (m-80) REVERT: A 109 MET cc_start: 0.2608 (pmm) cc_final: -0.0572 (ptt) REVERT: A 207 ILE cc_start: 0.8732 (mp) cc_final: 0.8390 (mm) REVERT: A 252 SER cc_start: 0.9248 (m) cc_final: 0.8840 (p) REVERT: A 513 TRP cc_start: 0.7468 (m-10) cc_final: 0.7079 (m-10) REVERT: A 522 GLU cc_start: 0.7855 (mm-30) cc_final: 0.6919 (pm20) REVERT: A 611 ASP cc_start: 0.7520 (m-30) cc_final: 0.7275 (m-30) REVERT: B 107 PHE cc_start: -0.0663 (OUTLIER) cc_final: -0.1629 (m-80) REVERT: B 109 MET cc_start: 0.2437 (pmm) cc_final: -0.0754 (ptt) REVERT: B 207 ILE cc_start: 0.8716 (mp) cc_final: 0.8374 (mm) REVERT: B 513 TRP cc_start: 0.7459 (m-10) cc_final: 0.7079 (m-10) REVERT: B 522 GLU cc_start: 0.7858 (mm-30) cc_final: 0.6926 (pm20) REVERT: B 611 ASP cc_start: 0.7501 (m-30) cc_final: 0.7271 (m-30) REVERT: C 107 PHE cc_start: -0.0660 (OUTLIER) cc_final: -0.1627 (m-80) REVERT: C 109 MET cc_start: 0.2450 (pmm) cc_final: -0.0761 (ptt) REVERT: C 207 ILE cc_start: 0.8773 (mp) cc_final: 0.8516 (mm) REVERT: C 252 SER cc_start: 0.9234 (m) cc_final: 0.8827 (p) REVERT: C 513 TRP cc_start: 0.7474 (m-10) cc_final: 0.7088 (m-10) REVERT: C 522 GLU cc_start: 0.7837 (mm-30) cc_final: 0.6932 (pm20) REVERT: C 611 ASP cc_start: 0.7513 (m-30) cc_final: 0.7277 (m-30) REVERT: D 107 PHE cc_start: -0.0681 (OUTLIER) cc_final: -0.1642 (m-80) REVERT: D 109 MET cc_start: 0.2580 (pmm) cc_final: -0.0618 (ptt) REVERT: D 207 ILE cc_start: 0.8705 (mp) cc_final: 0.8365 (mm) REVERT: D 252 SER cc_start: 0.9245 (m) cc_final: 0.8835 (p) REVERT: D 513 TRP cc_start: 0.7485 (m-10) cc_final: 0.7093 (m-10) REVERT: D 522 GLU cc_start: 0.7827 (mm-30) cc_final: 0.6927 (pm20) REVERT: D 611 ASP cc_start: 0.7533 (m-30) cc_final: 0.7287 (m-30) outliers start: 90 outliers final: 60 residues processed: 332 average time/residue: 0.2727 time to fit residues: 148.4221 Evaluate side-chains 333 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 269 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 620 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 118 optimal weight: 0.0870 chunk 174 optimal weight: 0.9980 chunk 263 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 209 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21804 Z= 0.199 Angle : 0.734 17.632 29584 Z= 0.384 Chirality : 0.045 0.237 3404 Planarity : 0.005 0.057 3668 Dihedral : 5.575 40.439 2864 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.15 % Favored : 85.78 % Rotamer: Outliers : 2.35 % Allowed : 24.58 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.17), residues: 2616 helix: 0.38 (0.16), residues: 1164 sheet: -2.79 (0.49), residues: 96 loop : -3.18 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 38 HIS 0.004 0.001 HIS B 539 PHE 0.036 0.002 PHE A 491 TYR 0.018 0.001 TYR A 508 ARG 0.008 0.000 ARG D 533 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 295 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7416 (tptt) cc_final: 0.6660 (tptt) REVERT: A 107 PHE cc_start: -0.0643 (OUTLIER) cc_final: -0.1772 (m-80) REVERT: A 109 MET cc_start: 0.2351 (pmm) cc_final: -0.1022 (ptt) REVERT: A 207 ILE cc_start: 0.8650 (mp) cc_final: 0.8330 (mm) REVERT: A 447 MET cc_start: 0.8752 (mtm) cc_final: 0.8396 (mtm) REVERT: A 513 TRP cc_start: 0.7409 (m-10) cc_final: 0.7042 (m-10) REVERT: A 522 GLU cc_start: 0.7850 (mm-30) cc_final: 0.6953 (pm20) REVERT: A 625 HIS cc_start: 0.7223 (m-70) cc_final: 0.6954 (m-70) REVERT: B 76 LYS cc_start: 0.7423 (tptt) cc_final: 0.6666 (tptt) REVERT: B 107 PHE cc_start: -0.0629 (OUTLIER) cc_final: -0.1759 (m-80) REVERT: B 109 MET cc_start: 0.2304 (pmm) cc_final: -0.1068 (ptt) REVERT: B 207 ILE cc_start: 0.8636 (mp) cc_final: 0.8315 (mm) REVERT: B 513 TRP cc_start: 0.7415 (m-10) cc_final: 0.7050 (m-10) REVERT: B 522 GLU cc_start: 0.7852 (mm-30) cc_final: 0.6953 (pm20) REVERT: B 625 HIS cc_start: 0.7228 (m-70) cc_final: 0.6962 (m-70) REVERT: C 76 LYS cc_start: 0.7408 (tptt) cc_final: 0.6657 (tptt) REVERT: C 107 PHE cc_start: -0.0621 (OUTLIER) cc_final: -0.1763 (m-80) REVERT: C 109 MET cc_start: 0.2313 (pmm) cc_final: -0.1080 (ptt) REVERT: C 207 ILE cc_start: 0.8650 (mp) cc_final: 0.8382 (mm) REVERT: C 447 MET cc_start: 0.8707 (mtm) cc_final: 0.8391 (mtm) REVERT: C 513 TRP cc_start: 0.7427 (m-10) cc_final: 0.7061 (m-10) REVERT: C 522 GLU cc_start: 0.7839 (mm-30) cc_final: 0.6983 (pm20) REVERT: C 625 HIS cc_start: 0.7235 (m-70) cc_final: 0.6969 (m-70) REVERT: C 658 ASN cc_start: 0.7659 (t0) cc_final: 0.7138 (p0) REVERT: D 76 LYS cc_start: 0.7393 (tptt) cc_final: 0.6647 (tptt) REVERT: D 107 PHE cc_start: -0.0643 (OUTLIER) cc_final: -0.1775 (m-80) REVERT: D 109 MET cc_start: 0.2328 (pmm) cc_final: -0.1058 (ptt) REVERT: D 207 ILE cc_start: 0.8626 (mp) cc_final: 0.8303 (mm) REVERT: D 447 MET cc_start: 0.8740 (mtm) cc_final: 0.8392 (mtm) REVERT: D 513 TRP cc_start: 0.7429 (m-10) cc_final: 0.7056 (m-10) REVERT: D 522 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6974 (pm20) REVERT: D 625 HIS cc_start: 0.7243 (m-70) cc_final: 0.6967 (m-70) outliers start: 56 outliers final: 44 residues processed: 335 average time/residue: 0.2699 time to fit residues: 149.0207 Evaluate side-chains 332 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 284 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 215 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 184 optimal weight: 0.0060 overall best weight: 2.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 473 GLN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 HIS ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS D 473 GLN ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.210056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.164004 restraints weight = 38590.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158308 restraints weight = 47306.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154483 restraints weight = 35949.753| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21804 Z= 0.382 Angle : 0.857 17.357 29584 Z= 0.448 Chirality : 0.050 0.263 3404 Planarity : 0.005 0.056 3668 Dihedral : 5.949 37.515 2864 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.92 % Allowed : 16.48 % Favored : 82.61 % Rotamer: Outliers : 2.82 % Allowed : 25.00 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.16), residues: 2616 helix: -0.07 (0.15), residues: 1188 sheet: -3.51 (0.78), residues: 48 loop : -3.27 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 38 HIS 0.004 0.001 HIS B 267 PHE 0.031 0.003 PHE C 491 TYR 0.033 0.003 TYR C 288 ARG 0.006 0.000 ARG C 533 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4257.76 seconds wall clock time: 82 minutes 4.27 seconds (4924.27 seconds total)