Starting phenix.real_space_refine on Sat Jul 4 03:29:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xdg_33147/07_2026/7xdg_33147.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xdg_33147/07_2026/7xdg_33147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xdg_33147/07_2026/7xdg_33147.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xdg_33147/07_2026/7xdg_33147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xdg_33147/07_2026/7xdg_33147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xdg_33147/07_2026/7xdg_33147.map" model { file = "/net/cci-nas-00/data/ceres_data/7xdg_33147/07_2026/7xdg_33147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xdg_33147/07_2026/7xdg_33147.cif" } resolution = 2.84 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= 0.064 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 11364 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 64 residue(s): 0.02s 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: 17836 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: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'D5S': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'D5S': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'D5S': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'D5S': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.35, per 1000 atoms: 0.19 Number of scatterers: 17836 At special positions: 0 Unit cell: (81.18, 135.3, 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 11364 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=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 739.7 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 54.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.960A pdb=" N MET A 29 " --> pdb=" O GLY A 25 " (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 Processing helix chain 'A' and resid 92 through 103 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.598A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.585A pdb=" N ILE A 146 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.686A pdb=" N GLY A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.527A 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: 3.521A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 247 removed outlier: 3.845A 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 280 through 298 removed outlier: 3.737A pdb=" N ALA A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.694A pdb=" N ASN A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.621A pdb=" N LYS A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.633A pdb=" N THR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 469 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 488 through 501 removed outlier: 3.649A pdb=" N LEU A 492 " --> pdb=" O ASP A 488 " (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 removed outlier: 3.568A pdb=" N VAL A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 removed outlier: 3.576A pdb=" N TYR A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.959A pdb=" N MET B 29 " --> pdb=" O GLY B 25 " (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 Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 103 through 112 removed outlier: 3.599A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 114 through 124 Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 142 through 149 removed outlier: 3.586A pdb=" N ILE B 146 " --> pdb=" O HIS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.685A pdb=" N GLY B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.527A 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: 3.522A pdb=" N LEU B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 247 removed outlier: 3.844A 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 280 through 298 removed outlier: 3.737A pdb=" N ALA B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 330 removed outlier: 3.694A pdb=" N ASN B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.622A pdb=" N LYS B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.633A pdb=" N THR B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 469 Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 488 through 501 removed outlier: 3.649A pdb=" N LEU B 492 " --> pdb=" O ASP B 488 " (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 removed outlier: 3.568A pdb=" N VAL B 522 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 557 removed outlier: 3.577A pdb=" N TYR B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.960A pdb=" N MET C 29 " --> pdb=" O GLY C 25 " (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 Processing helix chain 'C' and resid 92 through 103 Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.598A pdb=" N LEU C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 114 through 124 Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 142 through 149 removed outlier: 3.585A pdb=" N ILE C 146 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.685A pdb=" N GLY C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.527A 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: 3.522A pdb=" N LEU C 213 " --> pdb=" O ASN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 247 removed outlier: 3.844A 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 280 through 298 removed outlier: 3.736A pdb=" N ALA C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.695A pdb=" N ASN C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 removed outlier: 3.621A pdb=" N LYS C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 400 through 411 Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.633A pdb=" N THR C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 469 Processing helix chain 'C' and resid 470 through 482 Processing helix chain 'C' and resid 488 through 501 removed outlier: 3.649A pdb=" N LEU C 492 " --> pdb=" O ASP C 488 " (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 removed outlier: 3.568A pdb=" N VAL C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 557 removed outlier: 3.576A pdb=" N TYR C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 31 removed outlier: 3.959A pdb=" N MET D 29 " --> pdb=" O GLY D 25 " (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 Processing helix chain 'D' and resid 92 through 103 Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.599A pdb=" N LEU D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 114 through 124 Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 142 through 149 removed outlier: 3.584A pdb=" N ILE D 146 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.685A pdb=" N GLY D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.527A 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: 3.522A pdb=" N LEU D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 247 removed outlier: 3.844A 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 280 through 298 removed outlier: 3.736A pdb=" N ALA D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 330 removed outlier: 3.694A pdb=" N ASN D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 340 removed outlier: 3.622A pdb=" N LYS D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 400 through 411 Processing helix chain 'D' and resid 429 through 437 removed outlier: 3.632A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 469 Processing helix chain 'D' and resid 470 through 482 Processing helix chain 'D' and resid 488 through 501 removed outlier: 3.649A pdb=" N LEU D 492 " --> pdb=" O ASP D 488 " (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 removed outlier: 3.568A pdb=" N VAL D 522 " --> pdb=" O ASN D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 557 removed outlier: 3.575A pdb=" N TYR D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 136 removed outlier: 6.358A pdb=" N LEU A 133 " --> pdb=" O CYS A 202 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP A 204 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 135 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA A 157 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 201 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL A 159 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE A 203 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 161 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 158 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLU A 255 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 5.790A 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 343 removed outlier: 6.540A pdb=" N ILE A 307 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.359A pdb=" N LEU B 133 " --> pdb=" O CYS B 202 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP B 204 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 135 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 157 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 201 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 159 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE B 203 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR B 161 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 158 " --> pdb=" O GLN B 253 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU B 255 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 5.789A 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 343 removed outlier: 6.541A pdb=" N ILE B 307 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.359A pdb=" N LEU C 133 " --> pdb=" O CYS C 202 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP C 204 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE C 135 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA C 157 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL C 201 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL C 159 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE C 203 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR C 161 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 158 " --> pdb=" O GLN C 253 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLU C 255 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 5.790A 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 343 removed outlier: 6.540A pdb=" N ILE C 307 " --> pdb=" O TRP C 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 136 removed outlier: 6.359A pdb=" N LEU D 133 " --> pdb=" O CYS D 202 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP D 204 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 135 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA D 157 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL D 201 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL D 159 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE D 203 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR D 161 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 158 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU D 255 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 5.789A 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 343 removed outlier: 6.541A pdb=" N ILE D 307 " --> pdb=" O TRP D 342 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2220 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: 2.83 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2948 1.31 - 1.43: 4749 1.43 - 1.56: 10331 1.56 - 1.68: 72 1.68 - 1.81: 148 Bond restraints: 18248 Sorted by residual: bond pdb=" C2D NAD B 601 " pdb=" C3D NAD B 601 " ideal model delta sigma weight residual 1.531 1.233 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C2D NAD C 601 " pdb=" C3D NAD C 601 " ideal model delta sigma weight residual 1.531 1.233 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C2D NAD D 601 " pdb=" C3D NAD D 601 " ideal model delta sigma weight residual 1.531 1.233 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.233 0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C2D NAD B 602 " pdb=" C3D NAD B 602 " ideal model delta sigma weight residual 1.531 1.242 0.289 2.00e-02 2.50e+03 2.08e+02 ... (remaining 18243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 24303 2.69 - 5.38: 360 5.38 - 8.08: 73 8.08 - 10.77: 24 10.77 - 13.46: 20 Bond angle restraints: 24780 Sorted by residual: angle pdb=" O1A NAD C 601 " pdb=" PA NAD C 601 " pdb=" O2A NAD C 601 " ideal model delta sigma weight residual 122.64 109.18 13.46 3.00e+00 1.11e-01 2.01e+01 angle pdb=" O1A NAD B 601 " pdb=" PA NAD B 601 " pdb=" O2A NAD B 601 " ideal model delta sigma weight residual 122.64 109.21 13.43 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.21 13.43 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1A NAD D 601 " pdb=" PA NAD D 601 " pdb=" O2A NAD D 601 " ideal model delta sigma weight residual 122.64 109.22 13.42 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1A NAD A 602 " pdb=" PA NAD A 602 " pdb=" O2A NAD A 602 " ideal model delta sigma weight residual 122.64 109.53 13.11 3.00e+00 1.11e-01 1.91e+01 ... (remaining 24775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 9829 15.07 - 30.14: 839 30.14 - 45.22: 176 45.22 - 60.29: 20 60.29 - 75.36: 16 Dihedral angle restraints: 10880 sinusoidal: 4496 harmonic: 6384 Sorted by residual: dihedral pdb=" CA ASP A 256 " pdb=" C ASP A 256 " pdb=" N PHE A 257 " pdb=" CA PHE A 257 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP D 256 " pdb=" C ASP D 256 " pdb=" N PHE D 257 " pdb=" CA PHE D 257 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP B 256 " pdb=" C ASP B 256 " pdb=" N PHE B 257 " pdb=" CA PHE B 257 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 10877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2434 0.070 - 0.140: 258 0.140 - 0.210: 28 0.210 - 0.280: 4 0.280 - 0.350: 8 Chirality restraints: 2732 Sorted by residual: chirality pdb=" C3D NAD C 602 " pdb=" C2D NAD C 602 " pdb=" C4D NAD C 602 " pdb=" O3D NAD C 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C3D NAD B 602 " pdb=" C2D NAD B 602 " pdb=" C4D NAD B 602 " pdb=" O3D NAD B 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C3D NAD D 602 " pdb=" C2D NAD D 602 " pdb=" C4D NAD D 602 " pdb=" O3D NAD D 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2729 not shown) Planarity restraints: 3164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 527 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C ALA A 527 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA A 527 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 528 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 529 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LYS B 529 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS B 529 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 530 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 529 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LYS C 529 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS C 529 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 530 " 0.009 2.00e-02 2.50e+03 ... (remaining 3161 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 598 2.71 - 3.26: 18429 3.26 - 3.80: 29395 3.80 - 4.35: 37890 4.35 - 4.90: 64794 Nonbonded interactions: 151106 Sorted by model distance: nonbonded pdb=" OE2 GLU B 59 " pdb=" NH2 ARG B 67 " model vdw 2.160 3.120 nonbonded pdb=" OH TYR C 187 " pdb=" OE1 GLN C 253 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR B 187 " pdb=" OE1 GLN B 253 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR A 187 " pdb=" OE1 GLN A 253 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR D 187 " pdb=" OE1 GLN D 253 " model vdw 2.168 3.040 ... (remaining 151101 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: 0.06 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.130 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.014 0.298 18248 Z= 0.685 Angle : 0.908 13.460 24780 Z= 0.432 Chirality : 0.048 0.350 2732 Planarity : 0.004 0.033 3164 Dihedral : 11.973 75.361 6792 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.40 (0.17), residues: 2196 helix: 0.67 (0.15), residues: 1036 sheet: 0.26 (0.41), residues: 184 loop : -0.04 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 248 TYR 0.014 0.001 TYR C 552 PHE 0.021 0.002 PHE C 471 TRP 0.013 0.002 TRP C 342 HIS 0.003 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.01376 / 0.68 (18248) covalent geometry : angle 0.90778 / 0.43 (24780) hydrogen bonds : bond 0.15712 / 10.01 ( 752) hydrogen bonds : angle 6.89494 / 4.93 ( 2220) *********************** 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 185 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.692 Fit side-chains REVERT: A 248 ARG cc_start: 0.8128 (tpt170) cc_final: 0.7616 (mmm160) REVERT: A 336 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7004 (tp30) REVERT: A 405 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7461 (mtm180) REVERT: A 539 MET cc_start: 0.8286 (mtp) cc_final: 0.8062 (mtm) REVERT: B 248 ARG cc_start: 0.8113 (tpt170) cc_final: 0.7611 (mmm160) REVERT: B 336 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7004 (tp30) REVERT: B 405 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7507 (mtm180) REVERT: B 539 MET cc_start: 0.8293 (mtp) cc_final: 0.8057 (mtm) REVERT: C 248 ARG cc_start: 0.8115 (tpt170) cc_final: 0.7620 (mmm160) REVERT: C 336 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7002 (tp30) REVERT: C 405 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7487 (mtm180) REVERT: C 539 MET cc_start: 0.8297 (mtp) cc_final: 0.8071 (mtm) REVERT: D 248 ARG cc_start: 0.8114 (tpt170) cc_final: 0.7611 (mmm160) REVERT: D 336 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6993 (tp30) REVERT: D 405 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7484 (mtm180) REVERT: D 539 MET cc_start: 0.8296 (mtp) cc_final: 0.8055 (mtm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.5360 time to fit residues: 111.5027 Evaluate side-chains 133 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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: 1.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN B 43 GLN C 43 GLN D 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.145757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107349 restraints weight = 21954.535| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.80 r_work: 0.3274 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18248 Z= 0.162 Angle : 0.556 5.972 24780 Z= 0.288 Chirality : 0.042 0.200 2732 Planarity : 0.004 0.033 3164 Dihedral : 5.810 50.037 2508 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.07 % Allowed : 5.14 % Favored : 93.79 % 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 (0.17), residues: 2196 helix: 1.27 (0.16), residues: 1052 sheet: 0.07 (0.40), residues: 184 loop : 0.29 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 397 TYR 0.013 0.001 TYR C 552 PHE 0.021 0.002 PHE A 471 TRP 0.011 0.002 TRP D 558 HIS 0.004 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (18248) covalent geometry : angle 0.55551 / 0.29 (24780) hydrogen bonds : bond 0.04714 / 3.06 ( 752) hydrogen bonds : angle 4.95831 / 3.50 ( 2220) *********************** 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 159 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.535 Fit side-chains REVERT: A 248 ARG cc_start: 0.8111 (tpt170) cc_final: 0.7130 (mmm160) REVERT: A 332 LEU cc_start: 0.7177 (tt) cc_final: 0.6926 (tt) REVERT: A 335 GLN cc_start: 0.6250 (tp-100) cc_final: 0.6010 (tp-100) REVERT: A 336 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6910 (tp30) REVERT: A 405 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7496 (mtm180) REVERT: B 248 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7144 (mmm160) REVERT: B 335 GLN cc_start: 0.6285 (tp-100) cc_final: 0.6053 (tp-100) REVERT: B 336 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6830 (tp30) REVERT: B 405 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7525 (mtm180) REVERT: B 539 MET cc_start: 0.8188 (mtp) cc_final: 0.7775 (mtm) REVERT: C 248 ARG cc_start: 0.8103 (tpt170) cc_final: 0.7137 (mmm160) REVERT: C 335 GLN cc_start: 0.6258 (tp-100) cc_final: 0.6020 (tp-100) REVERT: C 336 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6831 (tp30) REVERT: C 405 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7535 (mtm180) REVERT: C 539 MET cc_start: 0.8203 (mtp) cc_final: 0.7788 (mtm) REVERT: D 248 ARG cc_start: 0.8111 (tpt170) cc_final: 0.7145 (mmm160) REVERT: D 335 GLN cc_start: 0.6249 (tp-100) cc_final: 0.6011 (tp-100) REVERT: D 336 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6829 (tp30) REVERT: D 405 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7525 (mtm180) outliers start: 20 outliers final: 8 residues processed: 155 average time/residue: 0.5308 time to fit residues: 92.7321 Evaluate side-chains 141 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 66 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.144321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105895 restraints weight = 22092.153| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.77 r_work: 0.3251 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18248 Z= 0.175 Angle : 0.546 6.071 24780 Z= 0.280 Chirality : 0.043 0.208 2732 Planarity : 0.004 0.035 3164 Dihedral : 5.525 53.853 2508 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.75 % Allowed : 8.57 % Favored : 90.69 % 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: 0.96 (0.17), residues: 2196 helix: 1.29 (0.16), residues: 1080 sheet: 0.00 (0.40), residues: 184 loop : 0.13 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.017 0.001 TYR A 187 PHE 0.022 0.002 PHE C 471 TRP 0.012 0.002 TRP D 558 HIS 0.004 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (18248) covalent geometry : angle 0.54625 / 0.28 (24780) hydrogen bonds : bond 0.04307 / 2.82 ( 752) hydrogen bonds : angle 4.63469 / 3.27 ( 2220) *********************** 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 158 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.699 Fit side-chains REVERT: A 248 ARG cc_start: 0.8119 (tpt170) cc_final: 0.7208 (mmm160) REVERT: A 332 LEU cc_start: 0.7180 (tt) cc_final: 0.6895 (tt) REVERT: A 335 GLN cc_start: 0.6341 (tp-100) cc_final: 0.6119 (tp-100) REVERT: A 336 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6877 (tp30) REVERT: A 405 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7344 (mtm-85) REVERT: A 539 MET cc_start: 0.8114 (mtp) cc_final: 0.7814 (mtm) REVERT: B 248 ARG cc_start: 0.8162 (tpt170) cc_final: 0.7240 (mmm160) REVERT: B 332 LEU cc_start: 0.7162 (tt) cc_final: 0.6874 (tt) REVERT: B 335 GLN cc_start: 0.6324 (tp-100) cc_final: 0.6111 (tp-100) REVERT: B 336 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6888 (tp30) REVERT: B 405 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: C 38 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8706 (mtm) REVERT: C 219 MET cc_start: 0.7724 (mtm) cc_final: 0.7236 (mtm) REVERT: C 248 ARG cc_start: 0.8156 (tpt170) cc_final: 0.7234 (mmm160) REVERT: C 332 LEU cc_start: 0.7161 (tt) cc_final: 0.6877 (tt) REVERT: C 335 GLN cc_start: 0.6325 (tp-100) cc_final: 0.6112 (tp-100) REVERT: C 336 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6873 (tp30) REVERT: C 405 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7377 (mtm-85) REVERT: D 248 ARG cc_start: 0.8133 (tpt170) cc_final: 0.7215 (mmm160) REVERT: D 332 LEU cc_start: 0.7169 (tt) cc_final: 0.6886 (tt) REVERT: D 335 GLN cc_start: 0.6342 (tp-100) cc_final: 0.6130 (tp-100) REVERT: D 336 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6872 (tp30) REVERT: D 405 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: D 539 MET cc_start: 0.8140 (mtp) cc_final: 0.7839 (mtm) outliers start: 14 outliers final: 8 residues processed: 156 average time/residue: 0.5245 time to fit residues: 92.5037 Evaluate side-chains 150 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 11 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.143639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105306 restraints weight = 22149.983| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.77 r_work: 0.3238 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18248 Z= 0.187 Angle : 0.551 6.356 24780 Z= 0.281 Chirality : 0.043 0.226 2732 Planarity : 0.004 0.031 3164 Dihedral : 5.449 57.012 2508 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.28 % Allowed : 9.10 % Favored : 89.61 % 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: 0.86 (0.17), residues: 2196 helix: 1.24 (0.16), residues: 1084 sheet: -0.14 (0.39), residues: 184 loop : 0.05 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.015 0.001 TYR A 187 PHE 0.023 0.002 PHE C 471 TRP 0.012 0.002 TRP D 558 HIS 0.003 0.001 HIS C 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (18248) covalent geometry : angle 0.55124 / 0.28 (24780) hydrogen bonds : bond 0.04268 / 2.80 ( 752) hydrogen bonds : angle 4.58733 / 3.24 ( 2220) *********************** 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 168 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.707 Fit side-chains REVERT: A 248 ARG cc_start: 0.8186 (tpt170) cc_final: 0.7313 (mmm160) REVERT: A 332 LEU cc_start: 0.7169 (tt) cc_final: 0.6885 (tt) REVERT: A 335 GLN cc_start: 0.6358 (tp-100) cc_final: 0.6133 (tp-100) REVERT: A 336 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6882 (tp30) REVERT: A 405 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7422 (mtm-85) REVERT: A 539 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7849 (mtm) REVERT: B 248 ARG cc_start: 0.8194 (tpt170) cc_final: 0.7317 (mmm160) REVERT: B 332 LEU cc_start: 0.7146 (tt) cc_final: 0.6910 (tt) REVERT: B 335 GLN cc_start: 0.6346 (tp-100) cc_final: 0.6123 (tp-100) REVERT: B 336 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6888 (tp30) REVERT: B 405 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7381 (mtm-85) REVERT: C 248 ARG cc_start: 0.8192 (tpt170) cc_final: 0.7311 (mmm160) REVERT: C 332 LEU cc_start: 0.7152 (tt) cc_final: 0.6917 (tt) REVERT: C 335 GLN cc_start: 0.6370 (tp-100) cc_final: 0.6148 (tp-100) REVERT: C 336 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6889 (tp30) REVERT: C 405 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7397 (mtm-85) REVERT: D 248 ARG cc_start: 0.8186 (tpt170) cc_final: 0.7306 (mmm160) REVERT: D 332 LEU cc_start: 0.7150 (tt) cc_final: 0.6903 (tt) REVERT: D 335 GLN cc_start: 0.6351 (tp-100) cc_final: 0.6127 (tp-100) REVERT: D 336 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6882 (tp30) REVERT: D 405 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7376 (mtm-85) REVERT: D 539 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7865 (mtm) outliers start: 24 outliers final: 15 residues processed: 160 average time/residue: 0.5179 time to fit residues: 93.3694 Evaluate side-chains 158 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 539 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 209 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 115 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 HIS B 260 HIS C 260 HIS D 260 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.147344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109234 restraints weight = 21886.580| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.85 r_work: 0.3287 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18248 Z= 0.116 Angle : 0.496 6.038 24780 Z= 0.253 Chirality : 0.041 0.226 2732 Planarity : 0.004 0.024 3164 Dihedral : 5.336 59.812 2508 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.28 % Allowed : 10.39 % Favored : 88.33 % 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 (0.17), residues: 2196 helix: 1.50 (0.16), residues: 1064 sheet: -0.16 (0.39), residues: 184 loop : 0.14 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 67 TYR 0.013 0.001 TYR A 187 PHE 0.020 0.001 PHE D 471 TRP 0.010 0.001 TRP C 558 HIS 0.002 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (18248) covalent geometry : angle 0.49606 / 0.25 (24780) hydrogen bonds : bond 0.03551 / 2.34 ( 752) hydrogen bonds : angle 4.35565 / 3.07 ( 2220) *********************** 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 179 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.715 Fit side-chains REVERT: A 248 ARG cc_start: 0.8104 (tpt170) cc_final: 0.7249 (mmm160) REVERT: A 332 LEU cc_start: 0.7207 (tt) cc_final: 0.6965 (tt) REVERT: A 335 GLN cc_start: 0.6264 (tp-100) cc_final: 0.6036 (tp-100) REVERT: A 336 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6849 (tp30) REVERT: A 405 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7469 (mtm-85) REVERT: B 248 ARG cc_start: 0.8104 (tpt170) cc_final: 0.7249 (mmm160) REVERT: B 405 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7385 (mtm-85) REVERT: C 248 ARG cc_start: 0.8101 (tpt170) cc_final: 0.7247 (mmm160) REVERT: C 332 LEU cc_start: 0.7190 (tt) cc_final: 0.6933 (tt) REVERT: C 335 GLN cc_start: 0.6312 (tp-100) cc_final: 0.6090 (tp-100) REVERT: C 336 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6800 (tp30) REVERT: C 405 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7407 (mtm-85) REVERT: D 248 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7243 (mmm160) REVERT: D 332 LEU cc_start: 0.7189 (tt) cc_final: 0.6934 (tt) REVERT: D 335 GLN cc_start: 0.6292 (tp-100) cc_final: 0.6069 (tp-100) REVERT: D 336 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6794 (tp30) REVERT: D 405 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7396 (mtm-85) outliers start: 24 outliers final: 10 residues processed: 174 average time/residue: 0.5150 time to fit residues: 101.1660 Evaluate side-chains 153 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 212 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.144947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106652 restraints weight = 21899.183| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.83 r_work: 0.3252 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18248 Z= 0.177 Angle : 0.552 8.509 24780 Z= 0.277 Chirality : 0.043 0.297 2732 Planarity : 0.004 0.025 3164 Dihedral : 5.288 58.415 2508 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.50 % Allowed : 11.30 % Favored : 87.21 % 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: 0.85 (0.17), residues: 2196 helix: 1.31 (0.16), residues: 1088 sheet: -0.23 (0.39), residues: 184 loop : -0.05 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.016 0.001 TYR C 187 PHE 0.022 0.002 PHE A 471 TRP 0.010 0.001 TRP D 558 HIS 0.002 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (18248) covalent geometry : angle 0.55162 / 0.28 (24780) hydrogen bonds : bond 0.04051 / 2.65 ( 752) hydrogen bonds : angle 4.48076 / 3.17 ( 2220) *********************** 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 169 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.8131 (tpt170) cc_final: 0.7286 (mmm160) REVERT: A 332 LEU cc_start: 0.7191 (tt) cc_final: 0.6962 (tt) REVERT: A 335 GLN cc_start: 0.6271 (tp-100) cc_final: 0.6040 (tp-100) REVERT: A 336 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6845 (tp30) REVERT: B 248 ARG cc_start: 0.8144 (tpt170) cc_final: 0.7300 (mmm160) REVERT: B 509 GLN cc_start: 0.7198 (mt0) cc_final: 0.6991 (mt0) REVERT: C 248 ARG cc_start: 0.8138 (tpt170) cc_final: 0.7293 (mmm160) REVERT: C 405 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7480 (mtm-85) REVERT: C 509 GLN cc_start: 0.7218 (mt0) cc_final: 0.7013 (mt0) REVERT: D 248 ARG cc_start: 0.8133 (tpt170) cc_final: 0.7291 (mmm160) REVERT: D 405 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7448 (mtm-85) outliers start: 28 outliers final: 14 residues processed: 166 average time/residue: 0.4828 time to fit residues: 91.1410 Evaluate side-chains 152 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.146534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108237 restraints weight = 21925.306| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.85 r_work: 0.3275 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18248 Z= 0.132 Angle : 0.519 7.458 24780 Z= 0.261 Chirality : 0.042 0.288 2732 Planarity : 0.004 0.027 3164 Dihedral : 5.187 56.287 2508 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.23 % Allowed : 11.62 % Favored : 87.15 % 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: 0.91 (0.17), residues: 2196 helix: 1.40 (0.16), residues: 1088 sheet: -0.19 (0.38), residues: 184 loop : -0.09 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 67 TYR 0.014 0.001 TYR D 187 PHE 0.020 0.001 PHE A 471 TRP 0.010 0.001 TRP B 558 HIS 0.002 0.001 HIS D 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (18248) covalent geometry : angle 0.51912 / 0.26 (24780) hydrogen bonds : bond 0.03665 / 2.41 ( 752) hydrogen bonds : angle 4.39489 / 3.11 ( 2220) *********************** 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 166 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.8106 (tpt170) cc_final: 0.7260 (mmm160) REVERT: A 425 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6150 (tm-30) REVERT: B 248 ARG cc_start: 0.8122 (tpt170) cc_final: 0.7267 (mmm160) REVERT: B 425 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6207 (tm-30) REVERT: C 248 ARG cc_start: 0.8110 (tpt170) cc_final: 0.7254 (mmm160) REVERT: C 425 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6234 (tm-30) REVERT: D 248 ARG cc_start: 0.8115 (tpt170) cc_final: 0.7261 (mmm160) REVERT: D 425 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6206 (tm-30) outliers start: 23 outliers final: 14 residues processed: 162 average time/residue: 0.5156 time to fit residues: 94.3471 Evaluate side-chains 158 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 154 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 192 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.146498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108306 restraints weight = 22043.520| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.86 r_work: 0.3277 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18248 Z= 0.129 Angle : 0.518 7.159 24780 Z= 0.261 Chirality : 0.042 0.268 2732 Planarity : 0.003 0.026 3164 Dihedral : 5.118 54.984 2508 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.09 % Allowed : 11.40 % Favored : 86.51 % 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 (0.17), residues: 2196 helix: 1.50 (0.16), residues: 1064 sheet: -0.18 (0.39), residues: 184 loop : -0.02 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.014 0.001 TYR C 187 PHE 0.020 0.001 PHE A 471 TRP 0.009 0.001 TRP D 558 HIS 0.002 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (18248) covalent geometry : angle 0.51776 / 0.26 (24780) hydrogen bonds : bond 0.03632 / 2.38 ( 752) hydrogen bonds : angle 4.36573 / 3.09 ( 2220) *********************** 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 180 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.8098 (tpt170) cc_final: 0.7263 (mmm160) REVERT: A 317 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6857 (mm) REVERT: A 425 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6170 (tm-30) REVERT: B 248 ARG cc_start: 0.8109 (tpt170) cc_final: 0.7266 (mmm160) REVERT: B 425 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6239 (tm-30) REVERT: C 248 ARG cc_start: 0.8102 (tpt170) cc_final: 0.7260 (mmm160) REVERT: C 425 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6276 (tm-30) REVERT: D 248 ARG cc_start: 0.8107 (tpt170) cc_final: 0.7268 (mmm160) REVERT: D 425 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6238 (tm-30) outliers start: 39 outliers final: 18 residues processed: 173 average time/residue: 0.5570 time to fit residues: 109.4994 Evaluate side-chains 163 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 190 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.145464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107160 restraints weight = 22050.470| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.85 r_work: 0.3261 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18248 Z= 0.160 Angle : 0.549 8.720 24780 Z= 0.276 Chirality : 0.043 0.309 2732 Planarity : 0.004 0.026 3164 Dihedral : 5.092 53.299 2508 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.61 % Allowed : 11.51 % Favored : 86.88 % 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: 0.87 (0.17), residues: 2196 helix: 1.37 (0.16), residues: 1088 sheet: -0.19 (0.39), residues: 184 loop : -0.12 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.015 0.001 TYR D 187 PHE 0.021 0.001 PHE D 471 TRP 0.010 0.001 TRP D 558 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (18248) covalent geometry : angle 0.54921 / 0.28 (24780) hydrogen bonds : bond 0.03899 / 2.56 ( 752) hydrogen bonds : angle 4.45349 / 3.15 ( 2220) *********************** 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 169 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7270 (mmm160) REVERT: A 425 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6160 (tm-30) REVERT: A 539 MET cc_start: 0.8072 (mtp) cc_final: 0.7803 (mtm) REVERT: B 248 ARG cc_start: 0.8121 (tpt170) cc_final: 0.7282 (mmm160) REVERT: B 317 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6906 (mm) REVERT: B 425 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6220 (tm-30) REVERT: C 248 ARG cc_start: 0.8118 (tpt170) cc_final: 0.7272 (mmm160) REVERT: C 317 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6906 (mm) REVERT: C 425 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6195 (tm-30) REVERT: D 248 ARG cc_start: 0.8117 (tpt170) cc_final: 0.7273 (mmm160) REVERT: D 317 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6891 (mm) REVERT: D 425 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6215 (tm-30) REVERT: D 539 MET cc_start: 0.8099 (mtp) cc_final: 0.7827 (mtm) outliers start: 30 outliers final: 16 residues processed: 162 average time/residue: 0.5556 time to fit residues: 102.2524 Evaluate side-chains 162 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 189 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 0.0270 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.146831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108618 restraints weight = 21828.702| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.85 r_work: 0.3283 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18248 Z= 0.125 Angle : 0.527 8.734 24780 Z= 0.264 Chirality : 0.042 0.318 2732 Planarity : 0.003 0.026 3164 Dihedral : 5.027 51.899 2508 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.50 % Allowed : 11.83 % Favored : 86.67 % 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: 1.06 (0.18), residues: 2196 helix: 1.57 (0.16), residues: 1060 sheet: -0.18 (0.39), residues: 184 loop : -0.00 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 129 TYR 0.014 0.001 TYR C 187 PHE 0.020 0.001 PHE A 471 TRP 0.009 0.001 TRP D 558 HIS 0.002 0.001 HIS D 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.12 (18248) covalent geometry : angle 0.52661 / 0.26 (24780) hydrogen bonds : bond 0.03598 / 2.37 ( 752) hydrogen bonds : angle 4.36011 / 3.08 ( 2220) ********************** 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 173 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.8102 (tpt170) cc_final: 0.7272 (mmm160) REVERT: A 317 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6860 (mm) REVERT: A 425 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: A 539 MET cc_start: 0.8036 (mtp) cc_final: 0.7758 (mtm) REVERT: B 248 ARG cc_start: 0.8106 (tpt170) cc_final: 0.7269 (mmm160) REVERT: B 317 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6882 (mm) REVERT: B 425 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6209 (tm-30) REVERT: C 248 ARG cc_start: 0.8103 (tpt170) cc_final: 0.7262 (mmm160) REVERT: C 317 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6880 (mm) REVERT: C 425 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6214 (tm-30) REVERT: D 248 ARG cc_start: 0.8097 (tpt170) cc_final: 0.7259 (mmm160) REVERT: D 317 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6869 (mm) REVERT: D 425 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6235 (tm-30) REVERT: D 539 MET cc_start: 0.8051 (mtp) cc_final: 0.7780 (mtm) outliers start: 28 outliers final: 17 residues processed: 162 average time/residue: 0.5472 time to fit residues: 100.0787 Evaluate side-chains 169 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 163 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.146555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.108247 restraints weight = 22132.699| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.87 r_work: 0.3276 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18248 Z= 0.137 Angle : 0.530 8.331 24780 Z= 0.266 Chirality : 0.042 0.309 2732 Planarity : 0.003 0.026 3164 Dihedral : 4.988 50.480 2508 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.50 % Allowed : 11.83 % Favored : 86.67 % 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: 1.54 (0.16), residues: 1064 sheet: -0.21 (0.39), residues: 184 loop : -0.06 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.014 0.001 TYR B 187 PHE 0.020 0.001 PHE A 471 TRP 0.008 0.001 TRP D 558 HIS 0.002 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18248) covalent geometry : angle 0.53000 / 0.27 (24780) hydrogen bonds : bond 0.03673 / 2.41 ( 752) hydrogen bonds : angle 4.37959 / 3.09 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3993.48 seconds wall clock time: 69 minutes 22.92 seconds (4162.92 seconds total)