Starting phenix.real_space_refine on Sat Jul 4 03:55:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xdf_33146/07_2026/7xdf_33146.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xdf_33146/07_2026/7xdf_33146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xdf_33146/07_2026/7xdf_33146.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xdf_33146/07_2026/7xdf_33146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xdf_33146/07_2026/7xdf_33146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xdf_33146/07_2026/7xdf_33146.map" model { file = "/net/cci-nas-00/data/ceres_data/7xdf_33146/07_2026/7xdf_33146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xdf_33146/07_2026/7xdf_33146.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.095 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 P 16 5.49 5 S 92 5.16 5 C 11396 2.51 5 N 3020 2.21 5 O 3344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17868 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "B" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "C" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "D" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.16, per 1000 atoms: 0.18 Number of scatterers: 17868 At special positions: 0 Unit cell: (77.9, 133.66, 133.66, 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) S 92 16.00 P 16 15.00 O 3344 8.00 N 3020 7.00 C 11396 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 - 3.00 Amino acid : True - 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 565.6 milliseconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4088 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 8 sheets defined 54.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.664A pdb=" N MET A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.609A pdb=" N PHE A 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 60 through 75 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.593A pdb=" N GLU A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 103 Processing helix chain 'A' and resid 103 through 112 Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.543A pdb=" N LEU A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.816A pdb=" N VAL A 181 " --> pdb=" O MET A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.572A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 247 removed outlier: 4.080A pdb=" N ASP A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 281 through 298 removed outlier: 3.598A pdb=" N LYS A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.618A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.526A pdb=" N ASN A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 466 through 469 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 487 through 501 removed outlier: 4.297A pdb=" N PHE A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 518 through 537 Processing helix chain 'A' and resid 548 through 557 removed outlier: 3.569A pdb=" N ARG A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.663A pdb=" N MET B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.609A pdb=" N PHE B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 60 through 75 Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.594A pdb=" N GLU B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 103 through 112 Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.543A pdb=" N LEU B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 148 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.816A pdb=" N VAL B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.573A pdb=" N LEU B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 247 removed outlier: 4.079A pdb=" N ASP B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.597A pdb=" N LYS B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 330 Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.617A pdb=" N LYS B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 400 through 411 removed outlier: 3.526A pdb=" N ASN B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 466 through 469 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 487 through 501 removed outlier: 4.297A pdb=" N PHE B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 548 through 557 removed outlier: 3.568A pdb=" N ARG B 556 " --> pdb=" O TYR B 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.664A pdb=" N MET C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.608A pdb=" N PHE C 40 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 60 through 75 Processing helix chain 'C' and resid 77 through 92 removed outlier: 3.593A pdb=" N GLU C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 Processing helix chain 'C' and resid 103 through 112 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.543A pdb=" N LEU C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.816A pdb=" N VAL C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.573A pdb=" N LEU C 213 " --> pdb=" O ASN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 247 removed outlier: 4.079A pdb=" N ASP C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 270 Processing helix chain 'C' and resid 281 through 298 removed outlier: 3.598A pdb=" N LYS C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 Processing helix chain 'C' and resid 333 through 339 removed outlier: 3.618A pdb=" N LYS C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 400 through 411 removed outlier: 3.526A pdb=" N ASN C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 466 through 469 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 487 through 501 removed outlier: 4.297A pdb=" N PHE C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 518 through 537 Processing helix chain 'C' and resid 548 through 557 removed outlier: 3.569A pdb=" N ARG C 556 " --> pdb=" O TYR C 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 31 removed outlier: 3.665A pdb=" N MET D 29 " --> pdb=" O GLY D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.609A pdb=" N PHE D 40 " --> pdb=" O GLY D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 60 through 75 Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.594A pdb=" N GLU D 90 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 103 Processing helix chain 'D' and resid 103 through 112 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 114 through 124 removed outlier: 3.543A pdb=" N LEU D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 148 Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.817A pdb=" N VAL D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.572A pdb=" N LEU D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 247 removed outlier: 4.079A pdb=" N ASP D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 270 Processing helix chain 'D' and resid 281 through 298 removed outlier: 3.597A pdb=" N LYS D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 330 Processing helix chain 'D' and resid 333 through 339 removed outlier: 3.617A pdb=" N LYS D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 400 through 411 removed outlier: 3.526A pdb=" N ASN D 411 " --> pdb=" O MET D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 Processing helix chain 'D' and resid 466 through 469 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 487 through 501 removed outlier: 4.296A pdb=" N PHE D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 510 Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 518 through 537 Processing helix chain 'D' and resid 548 through 557 removed outlier: 3.567A pdb=" N ARG D 556 " --> pdb=" O TYR D 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 136 removed outlier: 6.189A pdb=" N LEU A 133 " --> pdb=" O CYS A 202 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP A 204 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 135 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 157 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 201 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 159 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE A 203 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR A 161 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 158 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU A 255 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL A 160 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE A 307 " --> pdb=" O TRP A 342 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE A 344 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE A 309 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.188A pdb=" N LEU B 133 " --> pdb=" O CYS B 202 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP B 204 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 135 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA B 157 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL B 201 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 159 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE B 203 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR B 161 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 158 " --> pdb=" O GLN B 253 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU B 255 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL B 160 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE B 307 " --> pdb=" O TRP B 342 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE B 344 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE B 309 " --> pdb=" O PHE B 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.189A pdb=" N LEU C 133 " --> pdb=" O CYS C 202 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP C 204 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 135 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA C 157 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL C 201 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 159 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE C 203 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR C 161 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 158 " --> pdb=" O GLN C 253 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU C 255 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL C 160 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE C 307 " --> pdb=" O TRP C 342 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE C 344 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE C 309 " --> pdb=" O PHE C 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 136 removed outlier: 6.188A pdb=" N LEU D 133 " --> pdb=" O CYS D 202 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP D 204 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE D 135 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA D 157 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL D 201 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL D 159 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE D 203 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR D 161 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 158 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU D 255 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL D 160 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE D 307 " --> pdb=" O TRP D 342 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE D 344 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE D 309 " --> pdb=" O PHE D 344 " (cutoff:3.500A) 748 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: 2.25 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2948 1.31 - 1.43: 4782 1.43 - 1.56: 10338 1.56 - 1.68: 72 1.68 - 1.81: 148 Bond restraints: 18288 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.230 0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C2D NAD C 601 " pdb=" C3D NAD C 601 " ideal model delta sigma weight residual 1.531 1.231 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C2D NAD B 601 " pdb=" C3D NAD B 601 " ideal model delta sigma weight residual 1.531 1.231 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C2D NAD D 601 " pdb=" C3D NAD D 601 " ideal model delta sigma weight residual 1.531 1.231 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C2D NAD C 602 " pdb=" C3D NAD C 602 " ideal model delta sigma weight residual 1.531 1.237 0.294 2.00e-02 2.50e+03 2.16e+02 ... (remaining 18283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 24339 2.68 - 5.36: 391 5.36 - 8.03: 66 8.03 - 10.71: 32 10.71 - 13.39: 16 Bond angle restraints: 24844 Sorted by residual: angle pdb=" O1A NAD B 602 " pdb=" PA NAD B 602 " pdb=" O2A NAD B 602 " ideal model delta sigma weight residual 122.64 109.25 13.39 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O1A NAD C 602 " pdb=" PA NAD C 602 " pdb=" O2A NAD C 602 " ideal model delta sigma weight residual 122.64 109.26 13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O1A NAD B 601 " pdb=" PA NAD B 601 " pdb=" O2A NAD B 601 " ideal model delta sigma weight residual 122.64 109.28 13.36 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.29 13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O1A NAD C 601 " pdb=" PA NAD C 601 " pdb=" O2A NAD C 601 " ideal model delta sigma weight residual 122.64 109.29 13.35 3.00e+00 1.11e-01 1.98e+01 ... (remaining 24839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 9848 17.13 - 34.27: 888 34.27 - 51.40: 101 51.40 - 68.53: 29 68.53 - 85.67: 14 Dihedral angle restraints: 10880 sinusoidal: 4496 harmonic: 6384 Sorted by residual: dihedral pdb=" CA GLU C 304 " pdb=" C GLU C 304 " pdb=" N HIS C 305 " pdb=" CA HIS C 305 " ideal model delta harmonic sigma weight residual 180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU B 304 " pdb=" C GLU B 304 " pdb=" N HIS B 305 " pdb=" CA HIS B 305 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU A 304 " pdb=" C GLU A 304 " pdb=" N HIS A 305 " pdb=" CA HIS A 305 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 10877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2445 0.075 - 0.151: 257 0.151 - 0.226: 22 0.226 - 0.302: 4 0.302 - 0.377: 4 Chirality restraints: 2732 Sorted by residual: chirality pdb=" C4D NAD B 601 " pdb=" C3D NAD B 601 " pdb=" C5D NAD B 601 " pdb=" O4D NAD B 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C4D NAD C 601 " pdb=" C3D NAD C 601 " pdb=" C5D NAD C 601 " pdb=" O4D NAD C 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C4D NAD A 601 " pdb=" C3D NAD A 601 " pdb=" C5D NAD A 601 " pdb=" O4D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 2729 not shown) Planarity restraints: 3164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 26 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO B 27 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 26 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO C 27 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 26 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 27 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.027 5.00e-02 4.00e+02 ... (remaining 3161 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 250 2.63 - 3.20: 16531 3.20 - 3.77: 28042 3.77 - 4.33: 40932 4.33 - 4.90: 67949 Nonbonded interactions: 153704 Sorted by model distance: nonbonded pdb=" OD1 ASP A 236 " pdb=" OH TYR A 269 " model vdw 2.065 3.040 nonbonded pdb=" OD1 ASP C 236 " pdb=" OH TYR C 269 " model vdw 2.065 3.040 nonbonded pdb=" OD1 ASP B 236 " pdb=" OH TYR B 269 " model vdw 2.066 3.040 nonbonded pdb=" OD1 ASP D 236 " pdb=" OH TYR D 269 " model vdw 2.066 3.040 nonbonded pdb=" OE2 GLU B 59 " pdb=" NH2 ARG B 67 " model vdw 2.089 3.120 ... (remaining 153699 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.015 0.342 18304 Z= 0.926 Angle : 0.929 13.390 24844 Z= 0.432 Chirality : 0.049 0.377 2732 Planarity : 0.006 0.048 3164 Dihedral : 12.950 85.667 6792 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2196 helix: 0.35 (0.16), residues: 1036 sheet: 1.03 (0.36), residues: 204 loop : -0.02 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 405 TYR 0.013 0.001 TYR B 562 PHE 0.023 0.002 PHE D 471 TRP 0.009 0.001 TRP A 558 HIS 0.007 0.001 HIS C 305 Details of bonding type rmsd/Z covalent geometry : bond 0.01397 / 0.69 (18288) covalent geometry : angle 0.92930 / 0.43 (24844) hydrogen bonds : bond 0.17628 / 11.22 ( 748) hydrogen bonds : angle 6.96088 / 4.93 ( 2184) Misc. bond : bond 0.20771 / 10.86 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.463 Fit side-chains REVERT: A 152 GLU cc_start: 0.7477 (mp0) cc_final: 0.7190 (tp30) REVERT: A 314 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6767 (mm-30) REVERT: A 334 GLU cc_start: 0.7586 (tt0) cc_final: 0.7342 (tt0) REVERT: A 352 LYS cc_start: 0.5859 (mmpt) cc_final: 0.4650 (pttt) REVERT: A 359 ASP cc_start: 0.7526 (m-30) cc_final: 0.7264 (m-30) REVERT: A 398 LEU cc_start: 0.7420 (mm) cc_final: 0.7190 (mm) REVERT: A 460 PHE cc_start: 0.7819 (m-80) cc_final: 0.7421 (m-80) REVERT: A 488 ASP cc_start: 0.7397 (m-30) cc_final: 0.6964 (m-30) REVERT: A 565 LEU cc_start: 0.9033 (mt) cc_final: 0.8826 (mt) REVERT: B 29 MET cc_start: 0.8452 (mtp) cc_final: 0.8226 (mtp) REVERT: B 152 GLU cc_start: 0.7508 (mp0) cc_final: 0.7229 (tp30) REVERT: B 352 LYS cc_start: 0.5974 (mmpt) cc_final: 0.4766 (pttt) REVERT: B 359 ASP cc_start: 0.7523 (m-30) cc_final: 0.7279 (m-30) REVERT: B 460 PHE cc_start: 0.7770 (m-80) cc_final: 0.7390 (m-80) REVERT: B 488 ASP cc_start: 0.7374 (m-30) cc_final: 0.6958 (m-30) REVERT: C 29 MET cc_start: 0.8447 (mtp) cc_final: 0.8219 (mtp) REVERT: C 152 GLU cc_start: 0.7519 (mp0) cc_final: 0.7222 (tp30) REVERT: C 210 ILE cc_start: 0.8340 (pt) cc_final: 0.8138 (tp) REVERT: C 314 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6718 (mm-30) REVERT: C 352 LYS cc_start: 0.5933 (mmpt) cc_final: 0.4692 (pttt) REVERT: C 359 ASP cc_start: 0.7511 (m-30) cc_final: 0.7248 (m-30) REVERT: C 398 LEU cc_start: 0.7400 (mm) cc_final: 0.7180 (mm) REVERT: C 460 PHE cc_start: 0.7804 (m-80) cc_final: 0.7423 (m-80) REVERT: C 488 ASP cc_start: 0.7375 (m-30) cc_final: 0.6959 (m-30) REVERT: C 565 LEU cc_start: 0.9038 (mt) cc_final: 0.8835 (mt) REVERT: D 29 MET cc_start: 0.8408 (mtp) cc_final: 0.8176 (mtp) REVERT: D 152 GLU cc_start: 0.7472 (mp0) cc_final: 0.7205 (tp30) REVERT: D 314 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6758 (mm-30) REVERT: D 334 GLU cc_start: 0.7582 (tt0) cc_final: 0.7337 (tt0) REVERT: D 352 LYS cc_start: 0.5939 (mmpt) cc_final: 0.4717 (pttt) REVERT: D 359 ASP cc_start: 0.7539 (m-30) cc_final: 0.7291 (m-30) REVERT: D 398 LEU cc_start: 0.7419 (mm) cc_final: 0.7210 (mm) REVERT: D 460 PHE cc_start: 0.7805 (m-80) cc_final: 0.7400 (m-80) REVERT: D 488 ASP cc_start: 0.7377 (m-30) cc_final: 0.6948 (m-30) REVERT: D 565 LEU cc_start: 0.9039 (mt) cc_final: 0.8830 (mt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.5570 time to fit residues: 209.8499 Evaluate side-chains 229 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.0050 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 509 GLN B 61 GLN B 425 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN D 509 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105259 restraints weight = 20934.369| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.88 r_work: 0.3146 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18304 Z= 0.167 Angle : 0.614 6.807 24844 Z= 0.312 Chirality : 0.046 0.207 2732 Planarity : 0.005 0.045 3164 Dihedral : 6.356 57.427 2508 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.55 % Allowed : 9.58 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2196 helix: 0.90 (0.16), residues: 1060 sheet: 0.78 (0.34), residues: 204 loop : 0.21 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 91 TYR 0.012 0.001 TYR B 469 PHE 0.029 0.002 PHE B 471 TRP 0.011 0.001 TRP B 558 HIS 0.008 0.002 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (18288) covalent geometry : angle 0.61357 / 0.31 (24844) hydrogen bonds : bond 0.04948 / 3.24 ( 748) hydrogen bonds : angle 4.99685 / 3.50 ( 2184) Misc. bond : bond 0.00083 / 0.05 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8296 (tp) cc_final: 0.7965 (mt) REVERT: A 152 GLU cc_start: 0.8209 (mp0) cc_final: 0.7536 (mm-30) REVERT: A 314 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6916 (mm-30) REVERT: A 334 GLU cc_start: 0.7930 (tt0) cc_final: 0.7691 (tt0) REVERT: A 352 LYS cc_start: 0.6003 (mmpt) cc_final: 0.4749 (pttt) REVERT: A 359 ASP cc_start: 0.7753 (m-30) cc_final: 0.7485 (m-30) REVERT: A 460 PHE cc_start: 0.8033 (m-80) cc_final: 0.7638 (m-80) REVERT: B 118 LEU cc_start: 0.8239 (tp) cc_final: 0.7998 (tp) REVERT: B 152 GLU cc_start: 0.8270 (mp0) cc_final: 0.7566 (mm-30) REVERT: B 352 LYS cc_start: 0.6131 (mmpt) cc_final: 0.4858 (pttt) REVERT: B 359 ASP cc_start: 0.7796 (m-30) cc_final: 0.7565 (m-30) REVERT: B 460 PHE cc_start: 0.8054 (m-80) cc_final: 0.7675 (m-80) REVERT: C 152 GLU cc_start: 0.8271 (mp0) cc_final: 0.7565 (mm-30) REVERT: C 210 ILE cc_start: 0.8218 (pt) cc_final: 0.7920 (tp) REVERT: C 314 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6879 (mm-30) REVERT: C 352 LYS cc_start: 0.6070 (mmpt) cc_final: 0.4834 (pttt) REVERT: C 359 ASP cc_start: 0.7778 (m-30) cc_final: 0.7531 (m-30) REVERT: C 460 PHE cc_start: 0.8066 (m-80) cc_final: 0.7680 (m-80) REVERT: D 118 LEU cc_start: 0.8294 (tp) cc_final: 0.7962 (mt) REVERT: D 152 GLU cc_start: 0.8247 (mp0) cc_final: 0.7562 (mm-30) REVERT: D 314 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6931 (mm-30) REVERT: D 334 GLU cc_start: 0.7940 (tt0) cc_final: 0.7697 (tt0) REVERT: D 352 LYS cc_start: 0.5951 (mmpt) cc_final: 0.4728 (pttt) REVERT: D 359 ASP cc_start: 0.7772 (m-30) cc_final: 0.7447 (m-30) REVERT: D 363 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7137 (tm-30) REVERT: D 460 PHE cc_start: 0.8038 (m-80) cc_final: 0.7637 (m-80) outliers start: 29 outliers final: 4 residues processed: 239 average time/residue: 0.6400 time to fit residues: 169.0632 Evaluate side-chains 194 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 438 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 137 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 99 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101385 restraints weight = 20796.239| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.01 r_work: 0.3079 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18304 Z= 0.221 Angle : 0.625 6.223 24844 Z= 0.317 Chirality : 0.047 0.216 2732 Planarity : 0.005 0.042 3164 Dihedral : 6.171 53.253 2508 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.14 % Allowed : 12.37 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2196 helix: 0.77 (0.16), residues: 1072 sheet: 0.31 (0.32), residues: 204 loop : 0.14 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 405 TYR 0.013 0.002 TYR C 469 PHE 0.028 0.002 PHE C 471 TRP 0.010 0.001 TRP B 558 HIS 0.007 0.002 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.22 (18288) covalent geometry : angle 0.62543 / 0.32 (24844) hydrogen bonds : bond 0.05017 / 3.27 ( 748) hydrogen bonds : angle 4.86148 / 3.38 ( 2184) Misc. bond : bond 0.00133 / 0.07 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8424 (tp) cc_final: 0.8134 (mt) REVERT: A 352 LYS cc_start: 0.6061 (mmpt) cc_final: 0.4770 (pttt) REVERT: A 359 ASP cc_start: 0.7780 (m-30) cc_final: 0.7479 (m-30) REVERT: B 118 LEU cc_start: 0.8395 (tp) cc_final: 0.8109 (mt) REVERT: B 335 GLN cc_start: 0.7519 (tp40) cc_final: 0.7027 (mp10) REVERT: B 352 LYS cc_start: 0.6206 (mmpt) cc_final: 0.4879 (pttt) REVERT: B 359 ASP cc_start: 0.7812 (m-30) cc_final: 0.7529 (m-30) REVERT: C 210 ILE cc_start: 0.8271 (pt) cc_final: 0.7964 (tp) REVERT: C 335 GLN cc_start: 0.7467 (tp40) cc_final: 0.7004 (mp10) REVERT: C 352 LYS cc_start: 0.6151 (mmpt) cc_final: 0.4842 (pttt) REVERT: C 359 ASP cc_start: 0.7791 (m-30) cc_final: 0.7495 (m-30) REVERT: D 118 LEU cc_start: 0.8391 (tp) cc_final: 0.8098 (mt) REVERT: D 334 GLU cc_start: 0.7925 (tt0) cc_final: 0.7707 (tt0) REVERT: D 335 GLN cc_start: 0.7462 (tp40) cc_final: 0.7015 (mp10) REVERT: D 352 LYS cc_start: 0.6050 (mmpt) cc_final: 0.4784 (pttt) REVERT: D 359 ASP cc_start: 0.7783 (m-30) cc_final: 0.7469 (m-30) outliers start: 40 outliers final: 16 residues processed: 232 average time/residue: 0.5676 time to fit residues: 146.7212 Evaluate side-chains 184 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 149 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 177 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105619 restraints weight = 20680.814| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.86 r_work: 0.3145 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18304 Z= 0.117 Angle : 0.536 6.126 24844 Z= 0.272 Chirality : 0.043 0.209 2732 Planarity : 0.004 0.042 3164 Dihedral : 5.794 53.463 2508 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.36 % Allowed : 13.01 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2196 helix: 1.08 (0.16), residues: 1072 sheet: -0.09 (0.28), residues: 256 loop : 0.18 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.008 0.001 TYR C 112 PHE 0.022 0.002 PHE D 471 TRP 0.009 0.001 TRP B 558 HIS 0.006 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (18288) covalent geometry : angle 0.53629 / 0.27 (24844) hydrogen bonds : bond 0.03776 / 2.49 ( 748) hydrogen bonds : angle 4.52463 / 3.15 ( 2184) Misc. bond : bond 0.00103 / 0.05 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 LYS cc_start: 0.5991 (mmpt) cc_final: 0.4731 (pttt) REVERT: A 359 ASP cc_start: 0.7692 (m-30) cc_final: 0.7376 (m-30) REVERT: B 118 LEU cc_start: 0.8164 (tp) cc_final: 0.7929 (mt) REVERT: B 335 GLN cc_start: 0.7242 (tp40) cc_final: 0.6768 (mp10) REVERT: B 352 LYS cc_start: 0.6025 (mmpt) cc_final: 0.4759 (pttt) REVERT: B 359 ASP cc_start: 0.7734 (m-30) cc_final: 0.7416 (m-30) REVERT: B 432 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6722 (mt-10) REVERT: C 210 ILE cc_start: 0.8192 (pt) cc_final: 0.7885 (tp) REVERT: C 335 GLN cc_start: 0.7237 (tp40) cc_final: 0.6770 (mp10) REVERT: C 352 LYS cc_start: 0.5962 (mmpt) cc_final: 0.4734 (pttt) REVERT: C 359 ASP cc_start: 0.7686 (m-30) cc_final: 0.7371 (m-30) REVERT: D 335 GLN cc_start: 0.7193 (tp40) cc_final: 0.6763 (mp10) REVERT: D 352 LYS cc_start: 0.5879 (mmpt) cc_final: 0.4674 (pttt) REVERT: D 359 ASP cc_start: 0.7677 (m-30) cc_final: 0.7361 (m-30) REVERT: D 432 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6746 (mt-10) outliers start: 44 outliers final: 6 residues processed: 238 average time/residue: 0.5719 time to fit residues: 151.6035 Evaluate side-chains 185 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 8 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 206 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 69 optimal weight: 0.0970 chunk 180 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106139 restraints weight = 20507.566| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.85 r_work: 0.3147 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18304 Z= 0.114 Angle : 0.525 6.105 24844 Z= 0.265 Chirality : 0.042 0.211 2732 Planarity : 0.004 0.041 3164 Dihedral : 5.642 53.299 2508 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.03 % Allowed : 13.76 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2196 helix: 1.25 (0.16), residues: 1072 sheet: -0.05 (0.28), residues: 256 loop : 0.21 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 405 TYR 0.006 0.001 TYR C 112 PHE 0.028 0.002 PHE D 471 TRP 0.007 0.001 TRP D 558 HIS 0.005 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (18288) covalent geometry : angle 0.52521 / 0.27 (24844) hydrogen bonds : bond 0.03601 / 2.37 ( 748) hydrogen bonds : angle 4.40771 / 3.06 ( 2184) Misc. bond : bond 0.00104 / 0.05 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.672 Fit side-chains REVERT: A 336 GLU cc_start: 0.7266 (tp30) cc_final: 0.7058 (tp30) REVERT: A 352 LYS cc_start: 0.5973 (mmpt) cc_final: 0.4723 (pttt) REVERT: A 359 ASP cc_start: 0.7642 (m-30) cc_final: 0.7325 (m-30) REVERT: A 432 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6700 (mt-10) REVERT: A 501 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.6399 (mp10) REVERT: B 335 GLN cc_start: 0.7167 (tp40) cc_final: 0.6734 (mp10) REVERT: B 336 GLU cc_start: 0.7164 (tp30) cc_final: 0.6943 (tp30) REVERT: B 352 LYS cc_start: 0.6031 (mmpt) cc_final: 0.4806 (pttt) REVERT: B 359 ASP cc_start: 0.7618 (m-30) cc_final: 0.7323 (m-30) REVERT: B 501 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6372 (mp10) REVERT: C 210 ILE cc_start: 0.8172 (pt) cc_final: 0.7872 (tp) REVERT: C 335 GLN cc_start: 0.7172 (tp40) cc_final: 0.6771 (mp10) REVERT: C 336 GLU cc_start: 0.7157 (tp30) cc_final: 0.6934 (tp30) REVERT: C 352 LYS cc_start: 0.5975 (mmpt) cc_final: 0.4721 (pttt) REVERT: C 359 ASP cc_start: 0.7586 (m-30) cc_final: 0.7275 (m-30) REVERT: C 501 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.6389 (mp10) REVERT: D 335 GLN cc_start: 0.7117 (tp40) cc_final: 0.6754 (mp10) REVERT: D 336 GLU cc_start: 0.7172 (tp30) cc_final: 0.6948 (tp30) REVERT: D 352 LYS cc_start: 0.5835 (mmpt) cc_final: 0.4624 (pptt) REVERT: D 359 ASP cc_start: 0.7706 (m-30) cc_final: 0.7383 (m-30) REVERT: D 432 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6687 (mt-10) REVERT: D 501 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.6369 (mp10) outliers start: 38 outliers final: 9 residues processed: 219 average time/residue: 0.5869 time to fit residues: 143.1116 Evaluate side-chains 194 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 101 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 153 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104415 restraints weight = 20489.290| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.86 r_work: 0.3126 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18304 Z= 0.142 Angle : 0.539 6.107 24844 Z= 0.272 Chirality : 0.044 0.218 2732 Planarity : 0.004 0.039 3164 Dihedral : 5.631 51.079 2508 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.30 % Allowed : 14.13 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2196 helix: 1.29 (0.16), residues: 1076 sheet: -0.05 (0.28), residues: 256 loop : 0.16 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 227 TYR 0.010 0.001 TYR B 97 PHE 0.024 0.002 PHE B 471 TRP 0.008 0.001 TRP B 558 HIS 0.006 0.001 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (18288) covalent geometry : angle 0.53929 / 0.27 (24844) hydrogen bonds : bond 0.03864 / 2.53 ( 748) hydrogen bonds : angle 4.41924 / 3.07 ( 2184) Misc. bond : bond 0.00171 / 0.10 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.511 Fit side-chains REVERT: A 336 GLU cc_start: 0.7330 (tp30) cc_final: 0.7123 (tp30) REVERT: A 352 LYS cc_start: 0.5998 (mmpt) cc_final: 0.4703 (pptt) REVERT: A 359 ASP cc_start: 0.7672 (m-30) cc_final: 0.7370 (m-30) REVERT: A 432 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6721 (mt-10) REVERT: A 501 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.6480 (mp10) REVERT: B 335 GLN cc_start: 0.7197 (tp40) cc_final: 0.6726 (mp10) REVERT: B 336 GLU cc_start: 0.7211 (tp30) cc_final: 0.6964 (tp30) REVERT: B 352 LYS cc_start: 0.6096 (mmpt) cc_final: 0.4826 (pptt) REVERT: B 359 ASP cc_start: 0.7734 (m-30) cc_final: 0.7462 (m-30) REVERT: B 438 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6396 (pt0) REVERT: B 501 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.6333 (mp10) REVERT: C 210 ILE cc_start: 0.8206 (pt) cc_final: 0.7908 (tp) REVERT: C 335 GLN cc_start: 0.7182 (tp40) cc_final: 0.6730 (mp10) REVERT: C 336 GLU cc_start: 0.7178 (tp30) cc_final: 0.6924 (tp30) REVERT: C 352 LYS cc_start: 0.6055 (mmpt) cc_final: 0.4782 (pptt) REVERT: C 359 ASP cc_start: 0.7673 (m-30) cc_final: 0.7372 (m-30) REVERT: C 501 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.6423 (mp10) REVERT: D 335 GLN cc_start: 0.7169 (tp40) cc_final: 0.6744 (mp10) REVERT: D 336 GLU cc_start: 0.7233 (tp30) cc_final: 0.6972 (tp30) REVERT: D 352 LYS cc_start: 0.5949 (mmpt) cc_final: 0.4683 (pttt) REVERT: D 359 ASP cc_start: 0.7746 (m-30) cc_final: 0.7433 (m-30) REVERT: D 432 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6710 (mt-10) REVERT: D 501 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.6402 (mp10) outliers start: 43 outliers final: 12 residues processed: 223 average time/residue: 0.5762 time to fit residues: 142.8120 Evaluate side-chains 197 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 110 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 184 optimal weight: 0.8980 chunk 201 optimal weight: 0.0040 chunk 2 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106854 restraints weight = 20566.742| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.87 r_work: 0.3161 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18304 Z= 0.106 Angle : 0.511 6.075 24844 Z= 0.257 Chirality : 0.042 0.210 2732 Planarity : 0.004 0.039 3164 Dihedral : 5.384 49.100 2508 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.61 % Allowed : 14.88 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2196 helix: 1.40 (0.16), residues: 1080 sheet: -0.03 (0.29), residues: 256 loop : 0.09 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.007 0.001 TYR B 112 PHE 0.024 0.001 PHE D 471 TRP 0.008 0.001 TRP B 558 HIS 0.005 0.001 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (18288) covalent geometry : angle 0.51111 / 0.26 (24844) hydrogen bonds : bond 0.03367 / 2.22 ( 748) hydrogen bonds : angle 4.28839 / 2.98 ( 2184) Misc. bond : bond 0.00097 / 0.05 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.622 Fit side-chains REVERT: A 336 GLU cc_start: 0.7307 (tp30) cc_final: 0.6931 (tp30) REVERT: A 339 LYS cc_start: 0.7923 (mmtp) cc_final: 0.7566 (mmmm) REVERT: A 352 LYS cc_start: 0.6057 (mmpt) cc_final: 0.4778 (pptt) REVERT: A 359 ASP cc_start: 0.7667 (m-30) cc_final: 0.7385 (m-30) REVERT: A 432 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6672 (mt-10) REVERT: A 501 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.6300 (mp10) REVERT: B 335 GLN cc_start: 0.7124 (tp40) cc_final: 0.6545 (mp10) REVERT: B 336 GLU cc_start: 0.7154 (tp30) cc_final: 0.6844 (tp30) REVERT: B 339 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7519 (mmmm) REVERT: B 352 LYS cc_start: 0.6114 (mmpt) cc_final: 0.4818 (pptt) REVERT: B 359 ASP cc_start: 0.7674 (m-30) cc_final: 0.7388 (m-30) REVERT: B 432 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6665 (mt-10) REVERT: B 501 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.6269 (mp10) REVERT: C 47 MET cc_start: 0.8821 (ptp) cc_final: 0.8591 (ptp) REVERT: C 80 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7810 (mt-10) REVERT: C 210 ILE cc_start: 0.8174 (pt) cc_final: 0.7896 (tp) REVERT: C 336 GLU cc_start: 0.7141 (tp30) cc_final: 0.6859 (tp30) REVERT: C 352 LYS cc_start: 0.6075 (mmpt) cc_final: 0.4784 (pptt) REVERT: C 359 ASP cc_start: 0.7641 (m-30) cc_final: 0.7349 (m-30) REVERT: C 432 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6748 (mt-10) REVERT: C 501 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.6264 (mp10) REVERT: D 335 GLN cc_start: 0.7118 (tp40) cc_final: 0.6554 (mp10) REVERT: D 336 GLU cc_start: 0.7141 (tp30) cc_final: 0.6745 (tp30) REVERT: D 339 LYS cc_start: 0.8009 (mmtp) cc_final: 0.7625 (mmmm) REVERT: D 352 LYS cc_start: 0.5937 (mmpt) cc_final: 0.4705 (pttt) REVERT: D 359 ASP cc_start: 0.7670 (m-30) cc_final: 0.7361 (m-30) REVERT: D 432 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6655 (mt-10) outliers start: 30 outliers final: 14 residues processed: 217 average time/residue: 0.5898 time to fit residues: 141.9719 Evaluate side-chains 194 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 123 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 22 optimal weight: 0.0030 chunk 6 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 66 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 159 optimal weight: 0.0070 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN C 281 GLN D 281 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.139200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108787 restraints weight = 20985.120| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.90 r_work: 0.3189 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18304 Z= 0.098 Angle : 0.506 6.174 24844 Z= 0.253 Chirality : 0.042 0.202 2732 Planarity : 0.004 0.038 3164 Dihedral : 5.209 47.351 2508 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.23 % Allowed : 15.26 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2196 helix: 1.53 (0.16), residues: 1080 sheet: -0.02 (0.29), residues: 256 loop : 0.07 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 227 TYR 0.009 0.001 TYR C 187 PHE 0.020 0.001 PHE D 471 TRP 0.006 0.001 TRP B 558 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (18288) covalent geometry : angle 0.50577 / 0.25 (24844) hydrogen bonds : bond 0.03179 / 2.09 ( 748) hydrogen bonds : angle 4.16436 / 2.89 ( 2184) Misc. bond : bond 0.00092 / 0.05 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.708 Fit side-chains REVERT: A 80 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 336 GLU cc_start: 0.7321 (tp30) cc_final: 0.6933 (tp30) REVERT: A 339 LYS cc_start: 0.7903 (mmtp) cc_final: 0.7547 (mmmm) REVERT: A 352 LYS cc_start: 0.6071 (mmpt) cc_final: 0.4841 (pttt) REVERT: A 359 ASP cc_start: 0.7695 (m-30) cc_final: 0.7401 (m-30) REVERT: A 432 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6652 (mt-10) REVERT: A 501 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.6308 (mp10) REVERT: B 47 MET cc_start: 0.8822 (ptp) cc_final: 0.8582 (ptp) REVERT: B 335 GLN cc_start: 0.7135 (tp40) cc_final: 0.6917 (pp30) REVERT: B 336 GLU cc_start: 0.7190 (tp30) cc_final: 0.6854 (tp30) REVERT: B 339 LYS cc_start: 0.7821 (mmtp) cc_final: 0.7469 (mmmm) REVERT: B 352 LYS cc_start: 0.6121 (mmpt) cc_final: 0.4859 (pttt) REVERT: B 359 ASP cc_start: 0.7723 (m-30) cc_final: 0.7442 (m-30) REVERT: B 432 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6658 (mt-10) REVERT: B 501 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.6267 (mp10) REVERT: C 80 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7866 (mt-10) REVERT: C 210 ILE cc_start: 0.8138 (pt) cc_final: 0.7847 (tp) REVERT: C 336 GLU cc_start: 0.7172 (tp30) cc_final: 0.6823 (tp30) REVERT: C 352 LYS cc_start: 0.6132 (mmpt) cc_final: 0.4876 (pttt) REVERT: C 359 ASP cc_start: 0.7707 (m-30) cc_final: 0.7445 (m-30) REVERT: C 432 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6700 (mt-10) REVERT: D 80 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 335 GLN cc_start: 0.7116 (tp40) cc_final: 0.6888 (pp30) REVERT: D 336 GLU cc_start: 0.7163 (tp30) cc_final: 0.6839 (tp30) REVERT: D 339 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7605 (mmmm) REVERT: D 352 LYS cc_start: 0.5927 (mmpt) cc_final: 0.4758 (pttt) REVERT: D 359 ASP cc_start: 0.7676 (m-30) cc_final: 0.7411 (m-30) REVERT: D 385 LYS cc_start: 0.8491 (mppt) cc_final: 0.8278 (mmtt) REVERT: D 432 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6713 (mt-10) REVERT: D 501 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.6293 (mp10) outliers start: 23 outliers final: 13 residues processed: 221 average time/residue: 0.5932 time to fit residues: 145.8174 Evaluate side-chains 196 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 144 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107089 restraints weight = 20935.055| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.88 r_work: 0.3169 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18304 Z= 0.118 Angle : 0.520 6.473 24844 Z= 0.260 Chirality : 0.043 0.234 2732 Planarity : 0.004 0.038 3164 Dihedral : 5.206 44.146 2508 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.87 % Allowed : 15.20 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.18), residues: 2196 helix: 1.52 (0.16), residues: 1080 sheet: -0.04 (0.29), residues: 256 loop : 0.04 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 405 TYR 0.008 0.001 TYR C 187 PHE 0.026 0.001 PHE B 471 TRP 0.006 0.001 TRP B 558 HIS 0.005 0.001 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (18288) covalent geometry : angle 0.52034 / 0.26 (24844) hydrogen bonds : bond 0.03466 / 2.27 ( 748) hydrogen bonds : angle 4.23672 / 2.95 ( 2184) Misc. bond : bond 0.00097 / 0.05 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.674 Fit side-chains REVERT: A 336 GLU cc_start: 0.7316 (tp30) cc_final: 0.7004 (tp30) REVERT: A 339 LYS cc_start: 0.7919 (mmtp) cc_final: 0.7559 (mmmm) REVERT: A 352 LYS cc_start: 0.6136 (mmpt) cc_final: 0.4919 (pttt) REVERT: A 359 ASP cc_start: 0.7717 (m-30) cc_final: 0.7459 (m-30) REVERT: A 432 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6695 (mt-10) REVERT: A 501 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.6369 (mp10) REVERT: B 335 GLN cc_start: 0.7205 (tp40) cc_final: 0.6991 (pp30) REVERT: B 336 GLU cc_start: 0.7175 (tp30) cc_final: 0.6929 (tp30) REVERT: B 352 LYS cc_start: 0.6194 (mmpt) cc_final: 0.4936 (pttt) REVERT: B 359 ASP cc_start: 0.7730 (m-30) cc_final: 0.7467 (m-30) REVERT: B 432 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6652 (mt-10) REVERT: B 501 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.6370 (mp10) REVERT: C 80 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7912 (mt-10) REVERT: C 179 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7931 (mm) REVERT: C 210 ILE cc_start: 0.8131 (pt) cc_final: 0.7837 (tp) REVERT: C 336 GLU cc_start: 0.7264 (tp30) cc_final: 0.6925 (tp30) REVERT: C 352 LYS cc_start: 0.6118 (mmpt) cc_final: 0.4885 (pttt) REVERT: C 359 ASP cc_start: 0.7747 (m-30) cc_final: 0.7474 (m-30) REVERT: C 432 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6681 (mt-10) REVERT: C 501 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.6413 (mp10) REVERT: D 336 GLU cc_start: 0.7176 (tp30) cc_final: 0.6924 (tp30) REVERT: D 352 LYS cc_start: 0.5963 (mmpt) cc_final: 0.4778 (pttt) REVERT: D 359 ASP cc_start: 0.7696 (m-30) cc_final: 0.7416 (m-30) REVERT: D 432 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6694 (mt-10) REVERT: D 501 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.6372 (mp10) outliers start: 35 outliers final: 18 residues processed: 219 average time/residue: 0.5856 time to fit residues: 142.7628 Evaluate side-chains 197 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 91 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 115 optimal weight: 0.2980 chunk 113 optimal weight: 0.3980 chunk 136 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 214 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108601 restraints weight = 20802.109| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.88 r_work: 0.3199 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18304 Z= 0.103 Angle : 0.513 7.038 24844 Z= 0.257 Chirality : 0.043 0.247 2732 Planarity : 0.004 0.039 3164 Dihedral : 5.111 41.908 2508 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.34 % Allowed : 15.69 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2196 helix: 1.54 (0.16), residues: 1080 sheet: -0.02 (0.29), residues: 256 loop : 0.07 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.010 0.001 TYR A 112 PHE 0.023 0.001 PHE B 471 TRP 0.007 0.001 TRP B 558 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (18288) covalent geometry : angle 0.51318 / 0.26 (24844) hydrogen bonds : bond 0.03227 / 2.12 ( 748) hydrogen bonds : angle 4.17239 / 2.90 ( 2184) Misc. bond : bond 0.00093 / 0.05 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.536 Fit side-chains REVERT: A 336 GLU cc_start: 0.7373 (tp30) cc_final: 0.7073 (tp30) REVERT: A 339 LYS cc_start: 0.7906 (mmtp) cc_final: 0.7590 (mmmm) REVERT: A 352 LYS cc_start: 0.6257 (mmpt) cc_final: 0.5008 (pttt) REVERT: A 359 ASP cc_start: 0.7779 (m-30) cc_final: 0.7530 (m-30) REVERT: A 432 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 501 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.6448 (mp10) REVERT: B 336 GLU cc_start: 0.7208 (tp30) cc_final: 0.6965 (tp30) REVERT: B 352 LYS cc_start: 0.6320 (mmpt) cc_final: 0.5069 (pttt) REVERT: B 359 ASP cc_start: 0.7810 (m-30) cc_final: 0.7565 (m-30) REVERT: B 432 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6726 (mt-10) REVERT: B 501 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.6397 (mp10) REVERT: C 80 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8063 (mt-10) REVERT: C 210 ILE cc_start: 0.8193 (pt) cc_final: 0.7942 (tp) REVERT: C 336 GLU cc_start: 0.7350 (tp30) cc_final: 0.7023 (tp30) REVERT: C 352 LYS cc_start: 0.6258 (mmpt) cc_final: 0.5010 (pttt) REVERT: C 359 ASP cc_start: 0.7802 (m-30) cc_final: 0.7576 (m-30) REVERT: C 432 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6737 (mt-10) REVERT: C 501 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.6436 (mp10) REVERT: D 336 GLU cc_start: 0.7320 (tp30) cc_final: 0.6985 (tp30) REVERT: D 352 LYS cc_start: 0.6124 (mmpt) cc_final: 0.4889 (pttt) REVERT: D 359 ASP cc_start: 0.7785 (m-30) cc_final: 0.7531 (m-30) REVERT: D 385 LYS cc_start: 0.8549 (mppt) cc_final: 0.8286 (mmtt) REVERT: D 432 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6813 (mt-10) REVERT: D 501 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.6453 (mp10) outliers start: 25 outliers final: 16 residues processed: 205 average time/residue: 0.5874 time to fit residues: 133.6259 Evaluate side-chains 191 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 1 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106851 restraints weight = 20979.799| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.88 r_work: 0.3159 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18304 Z= 0.130 Angle : 0.532 6.982 24844 Z= 0.266 Chirality : 0.044 0.266 2732 Planarity : 0.004 0.039 3164 Dihedral : 5.149 41.201 2508 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.45 % Allowed : 16.11 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.18), residues: 2196 helix: 1.48 (0.16), residues: 1080 sheet: -0.07 (0.29), residues: 256 loop : 0.02 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 405 TYR 0.010 0.001 TYR A 112 PHE 0.026 0.002 PHE B 471 TRP 0.007 0.001 TRP B 558 HIS 0.005 0.001 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (18288) covalent geometry : angle 0.53204 / 0.27 (24844) hydrogen bonds : bond 0.03559 / 2.33 ( 748) hydrogen bonds : angle 4.22763 / 2.94 ( 2184) Misc. bond : bond 0.00093 / 0.05 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5049.48 seconds wall clock time: 86 minutes 52.49 seconds (5212.49 seconds total)