Starting phenix.real_space_refine on Thu Aug 8 00:48:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/08_2024/7yij_33860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/08_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_33860/08_2024/7yij_33860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/08_2024/7yij_33860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/08_2024/7yij_33860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yij_33860/08_2024/7yij_33860.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.72, per 1000 atoms: 0.55 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: 8.20 Conformation dependent library (CDL) restraints added in 3.7 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: 1.82 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: 5.47 Time building geometry restraints manager: 9.03 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 3.040 nonbonded pdb=" O GLY D 465 " pdb=" OG1 THR D 468 " model vdw 2.136 3.040 nonbonded pdb=" O GLY C 465 " pdb=" OG1 THR C 468 " model vdw 2.136 3.040 nonbonded pdb=" O GLY B 465 " pdb=" OG1 THR B 468 " model vdw 2.136 3.040 nonbonded pdb=" O THR D 512 " pdb=" OG SER D 516 " model vdw 2.144 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 3.570 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: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 54.180 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.650 ------------------------------------------------------------------------------- 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 : 2.290 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: 0.2817 time to fit residues: 149.2231 Evaluate side-chains 240 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.239 ------------------------------------------------------------------------------- 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: 0.8980 chunk 200 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 206 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 125 optimal weight: 0.1980 chunk 154 optimal weight: 0.2980 chunk 239 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 91 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 91 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 91 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 91 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 21804 Z= 0.216 Angle : 0.776 18.754 29584 Z= 0.412 Chirality : 0.047 0.279 3404 Planarity : 0.005 0.055 3668 Dihedral : 6.311 48.036 2864 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 1.38 % Allowed : 12.69 % Favored : 85.93 % Rotamer: Outliers : 1.34 % Allowed : 9.24 % Favored : 89.41 % 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: -2.39 (0.16), residues: 2616 helix: 0.28 (0.16), residues: 1132 sheet: -1.68 (0.61), residues: 88 loop : -3.39 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 38 HIS 0.004 0.001 HIS B 579 PHE 0.046 0.002 PHE B 676 TYR 0.013 0.001 TYR C 195 ARG 0.007 0.001 ARG C 677 *********************** 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 320 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 288 time to evaluate : 2.368 Fit side-chains REVERT: A 109 MET cc_start: 0.1679 (pmm) cc_final: 0.1318 (pmm) REVERT: A 270 PHE cc_start: 0.7500 (t80) cc_final: 0.7285 (t80) REVERT: A 506 MET cc_start: 0.8132 (tmm) cc_final: 0.7829 (tmm) REVERT: A 509 ILE cc_start: 0.8990 (pt) cc_final: 0.8764 (mm) REVERT: A 513 TRP cc_start: 0.7629 (m-10) cc_final: 0.7066 (m-10) REVERT: A 619 LYS cc_start: 0.7784 (mttt) cc_final: 0.7522 (mttt) REVERT: A 658 ASN cc_start: 0.6509 (t0) cc_final: 0.6305 (t0) REVERT: B 109 MET cc_start: 0.1644 (pmm) cc_final: 0.1281 (pmm) REVERT: B 270 PHE cc_start: 0.7508 (t80) cc_final: 0.7294 (t80) REVERT: B 506 MET cc_start: 0.8114 (tmm) cc_final: 0.7812 (tmm) REVERT: B 509 ILE cc_start: 0.8997 (pt) cc_final: 0.8772 (mm) REVERT: B 513 TRP cc_start: 0.7633 (m-10) cc_final: 0.7069 (m-10) REVERT: B 619 LYS cc_start: 0.7809 (mttt) cc_final: 0.7541 (mttt) REVERT: B 658 ASN cc_start: 0.6516 (t0) cc_final: 0.6310 (t0) REVERT: C 109 MET cc_start: 0.1617 (pmm) cc_final: 0.1257 (pmm) REVERT: C 270 PHE cc_start: 0.7505 (t80) cc_final: 0.7293 (t80) REVERT: C 506 MET cc_start: 0.8131 (tmm) cc_final: 0.7827 (tmm) REVERT: C 509 ILE cc_start: 0.8995 (pt) cc_final: 0.8773 (mm) REVERT: C 513 TRP cc_start: 0.7644 (m-10) cc_final: 0.7078 (m-10) REVERT: C 619 LYS cc_start: 0.7824 (mttt) cc_final: 0.7556 (mttt) REVERT: C 658 ASN cc_start: 0.6499 (t0) cc_final: 0.6290 (t0) REVERT: D 109 MET cc_start: 0.1651 (pmm) cc_final: 0.1296 (pmm) REVERT: D 270 PHE cc_start: 0.7507 (t80) cc_final: 0.7294 (t80) REVERT: D 506 MET cc_start: 0.8142 (tmm) cc_final: 0.7836 (tmm) REVERT: D 509 ILE cc_start: 0.8994 (pt) cc_final: 0.8770 (mm) REVERT: D 513 TRP cc_start: 0.7643 (m-10) cc_final: 0.7075 (m-10) REVERT: D 619 LYS cc_start: 0.7800 (mttt) cc_final: 0.7535 (mttt) REVERT: D 658 ASN cc_start: 0.6493 (t0) cc_final: 0.6285 (t0) outliers start: 32 outliers final: 28 residues processed: 308 average time/residue: 0.3079 time to fit residues: 154.2897 Evaluate side-chains 268 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 240 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP 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 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 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 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: 8.9990 chunk 74 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 0.0040 chunk 66 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 238 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- 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 477 ASN ** 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 ** 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 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** ** B 669 ASN ** 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 477 ASN ** 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 ** 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 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** ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 21804 Z= 0.478 Angle : 0.962 19.085 29584 Z= 0.502 Chirality : 0.055 0.288 3404 Planarity : 0.006 0.057 3668 Dihedral : 6.937 48.288 2864 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 1.38 % Allowed : 16.21 % Favored : 82.42 % Rotamer: Outliers : 3.19 % Allowed : 15.46 % Favored : 81.34 % 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: -2.78 (0.16), residues: 2616 helix: -0.24 (0.15), residues: 1144 sheet: -2.13 (0.53), residues: 88 loop : -3.41 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 618 HIS 0.009 0.002 HIS C 267 PHE 0.034 0.003 PHE C 613 TYR 0.024 0.003 TYR B 88 ARG 0.009 0.001 ARG D 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 324 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 248 time to evaluate : 2.160 Fit side-chains REVERT: A 109 MET cc_start: 0.2354 (pmm) cc_final: 0.1828 (pmm) REVERT: A 447 MET cc_start: 0.8778 (mtm) cc_final: 0.8346 (mtm) REVERT: A 506 MET cc_start: 0.8217 (tmm) cc_final: 0.7959 (tmm) REVERT: A 509 ILE cc_start: 0.8966 (pt) cc_final: 0.8705 (mm) REVERT: A 513 TRP cc_start: 0.7756 (m-10) cc_final: 0.7227 (m-10) REVERT: A 618 TRP cc_start: 0.5755 (p90) cc_final: 0.5250 (m-10) REVERT: B 109 MET cc_start: 0.2309 (pmm) cc_final: 0.1781 (pmm) REVERT: B 447 MET cc_start: 0.8700 (mtm) cc_final: 0.8327 (mtm) REVERT: B 506 MET cc_start: 0.8199 (tmm) cc_final: 0.7942 (tmm) REVERT: B 509 ILE cc_start: 0.8976 (pt) cc_final: 0.8714 (mm) REVERT: B 513 TRP cc_start: 0.7760 (m-10) cc_final: 0.7231 (m-10) REVERT: B 618 TRP cc_start: 0.5748 (p90) cc_final: 0.5254 (m-10) REVERT: C 109 MET cc_start: 0.2284 (pmm) cc_final: 0.1768 (pmm) REVERT: C 447 MET cc_start: 0.8740 (mtm) cc_final: 0.8347 (mtm) REVERT: C 506 MET cc_start: 0.8213 (tmm) cc_final: 0.7954 (tmm) REVERT: C 509 ILE cc_start: 0.8975 (pt) cc_final: 0.8714 (mm) REVERT: C 513 TRP cc_start: 0.7768 (m-10) cc_final: 0.7239 (m-10) REVERT: C 618 TRP cc_start: 0.5731 (p90) cc_final: 0.5255 (m-10) REVERT: D 109 MET cc_start: 0.2333 (pmm) cc_final: 0.1808 (pmm) REVERT: D 447 MET cc_start: 0.8763 (mtm) cc_final: 0.8343 (mtm) REVERT: D 506 MET cc_start: 0.8228 (tmm) cc_final: 0.7968 (tmm) REVERT: D 509 ILE cc_start: 0.8971 (pt) cc_final: 0.8711 (mm) REVERT: D 513 TRP cc_start: 0.7768 (m-10) cc_final: 0.7238 (m-10) REVERT: D 618 TRP cc_start: 0.5755 (p90) cc_final: 0.5254 (m-10) outliers start: 76 outliers final: 44 residues processed: 308 average time/residue: 0.2700 time to fit residues: 136.6391 Evaluate side-chains 284 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 240 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 277 VAL 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 612 VAL Chi-restraints excluded: chain B residue 58 VAL 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 277 VAL 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 612 VAL Chi-restraints excluded: chain C residue 58 VAL 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 277 VAL 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 612 VAL Chi-restraints excluded: chain D residue 58 VAL 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 277 VAL 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 612 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 20.0000 chunk 255 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 473 GLN A 477 ASN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS B 473 GLN B 477 ASN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS C 473 GLN C 477 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS D 473 GLN D 477 ASN ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3211 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: