Starting phenix.real_space_refine on Thu Mar 5 01:28:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xdg_33147/03_2026/7xdg_33147.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xdg_33147/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xdg_33147/03_2026/7xdg_33147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xdg_33147/03_2026/7xdg_33147.map" model { file = "/net/cci-nas-00/data/ceres_data/7xdg_33147/03_2026/7xdg_33147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xdg_33147/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.60, per 1000 atoms: 0.20 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: 1.97 Conformation dependent library (CDL) restraints added in 767.1 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: 0.55 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: 3.12 Time building geometry restraints manager: 1.84 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: 10017 15.07 - 30.14: 947 30.14 - 45.22: 220 45.22 - 60.29: 76 60.29 - 75.36: 20 Dihedral angle restraints: 11280 sinusoidal: 4896 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 11277 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: 5.310 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 13.272 75.361 7192 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 covalent geometry : bond 0.01376 (18248) covalent geometry : angle 0.90778 (24780) hydrogen bonds : bond 0.15712 ( 752) hydrogen bonds : angle 6.89494 ( 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 : 0.688 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: 0.5896 time to fit residues: 122.3762 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 : 0.626 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3862 r_free = 0.3862 target = 0.146125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107730 restraints weight = 21930.060| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.80 r_work: 0.3275 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18248 Z= 0.160 Angle : 0.559 6.007 24780 Z= 0.289 Chirality : 0.043 0.199 2732 Planarity : 0.004 0.033 3164 Dihedral : 9.101 53.892 2908 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.12 % Allowed : 5.14 % Favored : 93.74 % 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: 1.02 (0.17), residues: 2196 helix: 1.25 (0.16), residues: 1052 sheet: 0.08 (0.41), residues: 184 loop : 0.30 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 397 TYR 0.013 0.001 TYR D 552 PHE 0.021 0.002 PHE A 471 TRP 0.011 0.002 TRP A 558 HIS 0.004 0.001 HIS C 485 Details of bonding type rmsd covalent geometry : bond 0.00386 (18248) covalent geometry : angle 0.55877 (24780) hydrogen bonds : bond 0.04410 ( 752) hydrogen bonds : angle 4.85365 ( 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 163 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.583 Fit side-chains REVERT: A 248 ARG cc_start: 0.8096 (tpt170) cc_final: 0.7129 (mmm160) REVERT: A 332 LEU cc_start: 0.7166 (tt) cc_final: 0.6909 (tt) REVERT: A 335 GLN cc_start: 0.6339 (tp-100) cc_final: 0.6129 (tp-100) REVERT: A 336 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6907 (tp30) REVERT: A 405 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7500 (mtm180) REVERT: B 248 ARG cc_start: 0.8110 (tpt170) cc_final: 0.7147 (mmm160) REVERT: B 335 GLN cc_start: 0.6303 (tp-100) cc_final: 0.6094 (tp-100) REVERT: B 336 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6898 (tp30) REVERT: B 405 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7511 (mtm180) REVERT: C 248 ARG cc_start: 0.8103 (tpt170) cc_final: 0.7135 (mmm160) REVERT: C 335 GLN cc_start: 0.6296 (tp-100) cc_final: 0.6090 (tp-100) REVERT: C 336 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6846 (tp30) REVERT: C 405 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7523 (mtm180) REVERT: C 539 MET cc_start: 0.8128 (mtp) cc_final: 0.7739 (mtm) REVERT: D 248 ARG cc_start: 0.8102 (tpt170) cc_final: 0.7137 (mmm160) REVERT: D 335 GLN cc_start: 0.6280 (tp-100) cc_final: 0.6071 (tp-100) REVERT: D 336 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6845 (tp30) REVERT: D 405 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7511 (mtm180) REVERT: D 539 MET cc_start: 0.8164 (mtp) cc_final: 0.7774 (mtm) outliers start: 21 outliers final: 11 residues processed: 158 average time/residue: 0.5974 time to fit residues: 105.8792 Evaluate side-chains 145 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 504 ASP 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 196 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP 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: 3.9990 chunk 7 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104498 restraints weight = 22189.799| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.76 r_work: 0.3229 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18248 Z= 0.215 Angle : 0.575 6.105 24780 Z= 0.295 Chirality : 0.044 0.225 2732 Planarity : 0.004 0.031 3164 Dihedral : 8.117 55.028 2908 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.12 % Allowed : 8.89 % Favored : 89.99 % 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: 0.82 (0.17), residues: 2196 helix: 1.16 (0.16), residues: 1084 sheet: -0.12 (0.39), residues: 184 loop : 0.09 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 270 TYR 0.017 0.002 TYR D 187 PHE 0.024 0.002 PHE C 471 TRP 0.013 0.002 TRP D 558 HIS 0.003 0.001 HIS D 485 Details of bonding type rmsd covalent geometry : bond 0.00536 (18248) covalent geometry : angle 0.57491 (24780) hydrogen bonds : bond 0.04691 ( 752) hydrogen bonds : angle 4.74825 ( 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 162 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.678 Fit side-chains REVERT: A 219 MET cc_start: 0.7820 (mtm) cc_final: 0.7374 (mtm) REVERT: A 248 ARG cc_start: 0.8175 (tpt170) cc_final: 0.7257 (mmm160) REVERT: A 332 LEU cc_start: 0.7158 (tt) cc_final: 0.6861 (tt) REVERT: A 335 GLN cc_start: 0.6343 (tp-100) cc_final: 0.6125 (tp-100) REVERT: A 336 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6884 (tp30) REVERT: A 405 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7354 (mtm-85) REVERT: B 248 ARG cc_start: 0.8179 (tpt170) cc_final: 0.7266 (mmm160) REVERT: B 332 LEU cc_start: 0.7131 (tt) cc_final: 0.6852 (tt) REVERT: B 335 GLN cc_start: 0.6351 (tp-100) cc_final: 0.6138 (tp-100) REVERT: B 336 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6888 (tp30) REVERT: B 405 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7333 (mtm-85) REVERT: C 248 ARG cc_start: 0.8172 (tpt170) cc_final: 0.7257 (mmm160) REVERT: C 332 LEU cc_start: 0.7155 (tt) cc_final: 0.6874 (tt) REVERT: C 335 GLN cc_start: 0.6351 (tp-100) cc_final: 0.6140 (tp-100) REVERT: C 336 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6886 (tp30) REVERT: C 405 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7353 (mtm-85) REVERT: D 248 ARG cc_start: 0.8177 (tpt170) cc_final: 0.7261 (mmm160) REVERT: D 332 LEU cc_start: 0.7149 (tt) cc_final: 0.6869 (tt) REVERT: D 335 GLN cc_start: 0.6337 (tp-100) cc_final: 0.6123 (tp-100) REVERT: D 336 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6884 (tp30) REVERT: D 405 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7318 (mtm-85) outliers start: 21 outliers final: 9 residues processed: 158 average time/residue: 0.5972 time to fit residues: 105.7897 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 : 0.450 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 504 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 11 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 219 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS B 260 HIS C 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.145945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107376 restraints weight = 22016.927| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.82 r_work: 0.3268 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1427 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 : 0.514 7.368 24780 Z= 0.262 Chirality : 0.042 0.277 2732 Planarity : 0.004 0.029 3164 Dihedral : 7.706 59.987 2908 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.91 % Allowed : 9.31 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2196 helix: 1.32 (0.16), residues: 1088 sheet: -0.10 (0.39), residues: 184 loop : 0.08 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 67 TYR 0.013 0.001 TYR A 187 PHE 0.021 0.001 PHE A 471 TRP 0.010 0.001 TRP D 558 HIS 0.003 0.001 HIS C 485 Details of bonding type rmsd covalent geometry : bond 0.00321 (18248) covalent geometry : angle 0.51419 (24780) hydrogen bonds : bond 0.03787 ( 752) hydrogen bonds : angle 4.46368 ( 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 166 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.649 Fit side-chains REVERT: A 248 ARG cc_start: 0.8099 (tpt170) cc_final: 0.7228 (mmm160) REVERT: A 332 LEU cc_start: 0.7185 (tt) cc_final: 0.6928 (tt) REVERT: A 335 GLN cc_start: 0.6311 (tp-100) cc_final: 0.6083 (tp-100) REVERT: A 336 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6841 (tp30) REVERT: A 405 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7381 (mtm-85) REVERT: A 539 MET cc_start: 0.8047 (mtm) cc_final: 0.7817 (mtp) REVERT: B 248 ARG cc_start: 0.8119 (tpt170) cc_final: 0.7231 (mmm160) REVERT: B 332 LEU cc_start: 0.7184 (tt) cc_final: 0.6939 (tt) REVERT: B 335 GLN cc_start: 0.6297 (tp-100) cc_final: 0.6079 (tp-100) REVERT: B 336 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6865 (tp30) REVERT: B 405 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: C 248 ARG cc_start: 0.8095 (tpt170) cc_final: 0.7225 (mmm160) REVERT: C 332 LEU cc_start: 0.7174 (tt) cc_final: 0.6923 (tt) REVERT: C 335 GLN cc_start: 0.6282 (tp-100) cc_final: 0.6067 (tp-100) REVERT: C 336 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6862 (tp30) REVERT: C 405 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7391 (mtm-85) REVERT: D 248 ARG cc_start: 0.8115 (tpt170) cc_final: 0.7220 (mmm160) REVERT: D 332 LEU cc_start: 0.7170 (tt) cc_final: 0.6909 (tt) REVERT: D 335 GLN cc_start: 0.6308 (tp-100) cc_final: 0.6085 (tp-100) REVERT: D 336 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6860 (tp30) REVERT: D 405 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7377 (mtm-85) outliers start: 17 outliers final: 15 residues processed: 165 average time/residue: 0.5699 time to fit residues: 105.6389 Evaluate side-chains 160 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 209 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 260 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109199 restraints weight = 21812.603| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.85 r_work: 0.3286 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1540 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= 0.123 Angle : 0.492 6.010 24780 Z= 0.251 Chirality : 0.041 0.215 2732 Planarity : 0.004 0.027 3164 Dihedral : 7.313 57.071 2908 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.34 % Allowed : 10.60 % Favored : 88.06 % 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: 1.07 (0.17), residues: 2196 helix: 1.48 (0.16), residues: 1068 sheet: -0.17 (0.39), residues: 184 loop : 0.12 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 67 TYR 0.013 0.001 TYR D 187 PHE 0.020 0.001 PHE C 471 TRP 0.008 0.001 TRP D 558 HIS 0.002 0.001 HIS C 485 Details of bonding type rmsd covalent geometry : bond 0.00298 (18248) covalent geometry : angle 0.49196 (24780) hydrogen bonds : bond 0.03573 ( 752) hydrogen bonds : angle 4.32533 ( 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 180 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 248 ARG cc_start: 0.8135 (tpt170) cc_final: 0.7287 (mmm160) REVERT: A 332 LEU cc_start: 0.7232 (tt) cc_final: 0.7021 (tt) REVERT: A 335 GLN cc_start: 0.6226 (tp-100) cc_final: 0.5990 (tp-100) REVERT: A 336 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6793 (tp30) REVERT: A 539 MET cc_start: 0.8068 (mtm) cc_final: 0.7857 (mtp) REVERT: B 219 MET cc_start: 0.7859 (mtm) cc_final: 0.7601 (mtm) REVERT: B 248 ARG cc_start: 0.8149 (tpt170) cc_final: 0.7298 (mmm160) REVERT: B 332 LEU cc_start: 0.7203 (tt) cc_final: 0.6994 (tt) REVERT: B 335 GLN cc_start: 0.6312 (tp-100) cc_final: 0.6089 (tp-100) REVERT: B 336 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6799 (tp30) REVERT: B 405 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7393 (mtm-85) REVERT: B 539 MET cc_start: 0.7984 (mtm) cc_final: 0.7746 (mtp) REVERT: C 248 ARG cc_start: 0.8137 (tpt170) cc_final: 0.7284 (mmm160) REVERT: C 332 LEU cc_start: 0.7197 (tt) cc_final: 0.6974 (tt) REVERT: C 335 GLN cc_start: 0.6312 (tp-100) cc_final: 0.6090 (tp-100) REVERT: C 336 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6794 (tp30) REVERT: C 405 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7398 (mtm-85) REVERT: D 219 MET cc_start: 0.7848 (mtm) cc_final: 0.7593 (mtm) REVERT: D 248 ARG cc_start: 0.8140 (tpt170) cc_final: 0.7286 (mmm160) REVERT: D 332 LEU cc_start: 0.7207 (tt) cc_final: 0.6995 (tt) REVERT: D 335 GLN cc_start: 0.6301 (tp-100) cc_final: 0.6077 (tp-100) REVERT: D 336 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6796 (tp30) REVERT: D 405 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7398 (mtm-85) outliers start: 25 outliers final: 12 residues processed: 175 average time/residue: 0.5787 time to fit residues: 113.6273 Evaluate side-chains 156 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 201 optimal weight: 0.0070 chunk 138 optimal weight: 0.2980 chunk 87 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.146755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108280 restraints weight = 21756.839| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.80 r_work: 0.3285 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18248 Z= 0.130 Angle : 0.511 8.038 24780 Z= 0.257 Chirality : 0.042 0.284 2732 Planarity : 0.003 0.025 3164 Dihedral : 7.185 56.597 2908 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.28 % Allowed : 11.30 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2196 helix: 1.41 (0.16), residues: 1092 sheet: -0.22 (0.39), residues: 184 loop : -0.04 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 67 TYR 0.014 0.001 TYR C 187 PHE 0.020 0.001 PHE A 471 TRP 0.008 0.001 TRP D 558 HIS 0.002 0.001 HIS C 485 Details of bonding type rmsd covalent geometry : bond 0.00320 (18248) covalent geometry : angle 0.51115 (24780) hydrogen bonds : bond 0.03599 ( 752) hydrogen bonds : angle 4.34830 ( 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 163 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7526 (mmm) cc_final: 0.7165 (mtm) REVERT: A 248 ARG cc_start: 0.8104 (tpt170) cc_final: 0.7254 (mmm160) REVERT: A 539 MET cc_start: 0.8075 (mtm) cc_final: 0.7845 (mtp) REVERT: B 239 MET cc_start: 0.7532 (mmm) cc_final: 0.7179 (mtm) REVERT: B 248 ARG cc_start: 0.8128 (tpt170) cc_final: 0.7277 (mmm160) REVERT: B 539 MET cc_start: 0.8052 (mtm) cc_final: 0.7814 (mtp) REVERT: C 239 MET cc_start: 0.7530 (mmm) cc_final: 0.7174 (mtm) REVERT: C 248 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7261 (mmm160) REVERT: D 239 MET cc_start: 0.7527 (mmm) cc_final: 0.7170 (mtm) REVERT: D 248 ARG cc_start: 0.8116 (tpt170) cc_final: 0.7258 (mmm160) outliers start: 24 outliers final: 16 residues processed: 162 average time/residue: 0.5342 time to fit residues: 97.8628 Evaluate side-chains 150 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU 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 50 LEU 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 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 467 ASN Chi-restraints excluded: chain D residue 50 LEU 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: 0.8980 chunk 176 optimal weight: 0.0970 chunk 189 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 115 optimal weight: 0.0050 chunk 35 optimal weight: 0.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110860 restraints weight = 21817.457| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.86 r_work: 0.3313 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1742 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= 0.107 Angle : 0.494 7.200 24780 Z= 0.250 Chirality : 0.041 0.273 2732 Planarity : 0.003 0.024 3164 Dihedral : 7.013 55.137 2908 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.45 % Allowed : 11.56 % Favored : 86.99 % 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: 1.15 (0.18), residues: 2196 helix: 1.61 (0.16), residues: 1064 sheet: -0.19 (0.39), residues: 184 loop : 0.09 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.013 0.001 TYR D 187 PHE 0.018 0.001 PHE D 471 TRP 0.007 0.001 TRP A 558 HIS 0.002 0.001 HIS C 485 Details of bonding type rmsd covalent geometry : bond 0.00255 (18248) covalent geometry : angle 0.49434 (24780) hydrogen bonds : bond 0.03324 ( 752) hydrogen bonds : angle 4.26322 ( 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 172 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7745 (mtm) cc_final: 0.7505 (mtm) REVERT: A 239 MET cc_start: 0.7489 (mmm) cc_final: 0.7143 (mtm) REVERT: A 248 ARG cc_start: 0.8103 (tpt170) cc_final: 0.7262 (mmm160) REVERT: A 425 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6158 (tm-30) REVERT: A 539 MET cc_start: 0.7967 (mtm) cc_final: 0.7720 (mtp) REVERT: B 239 MET cc_start: 0.7536 (mmm) cc_final: 0.7195 (mtm) REVERT: B 248 ARG cc_start: 0.8118 (tpt170) cc_final: 0.7264 (mmm160) REVERT: B 425 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6231 (tm-30) REVERT: B 539 MET cc_start: 0.7991 (mtm) cc_final: 0.7732 (mtp) REVERT: C 239 MET cc_start: 0.7516 (mmm) cc_final: 0.7166 (mtm) REVERT: C 248 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7250 (mmm160) REVERT: C 425 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.6211 (tm-30) REVERT: D 239 MET cc_start: 0.7518 (mmm) cc_final: 0.7171 (mtm) REVERT: D 248 ARG cc_start: 0.8114 (tpt170) cc_final: 0.7262 (mmm160) REVERT: D 317 LEU cc_start: 0.7290 (mm) cc_final: 0.6870 (mm) REVERT: D 425 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6240 (tm-30) REVERT: D 509 GLN cc_start: 0.7015 (mt0) cc_final: 0.6772 (mt0) outliers start: 27 outliers final: 16 residues processed: 168 average time/residue: 0.5650 time to fit residues: 106.8904 Evaluate side-chains 160 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU 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 50 LEU 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 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 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: 3.9990 chunk 122 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 148 optimal weight: 0.0270 chunk 117 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN B 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.147932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109528 restraints weight = 21919.530| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.83 r_work: 0.3305 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18248 Z= 0.116 Angle : 0.500 6.138 24780 Z= 0.253 Chirality : 0.041 0.252 2732 Planarity : 0.003 0.024 3164 Dihedral : 6.911 55.022 2908 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.66 % Allowed : 11.51 % Favored : 86.83 % 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: 1.09 (0.18), residues: 2196 helix: 1.62 (0.16), residues: 1064 sheet: -0.18 (0.39), residues: 184 loop : -0.03 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.013 0.001 TYR C 187 PHE 0.019 0.001 PHE A 471 TRP 0.007 0.001 TRP D 558 HIS 0.002 0.001 HIS C 485 Details of bonding type rmsd covalent geometry : bond 0.00282 (18248) covalent geometry : angle 0.50019 (24780) hydrogen bonds : bond 0.03381 ( 752) hydrogen bonds : angle 4.26102 ( 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 175 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7499 (mmm) cc_final: 0.7142 (mtm) REVERT: A 248 ARG cc_start: 0.8093 (tpt170) cc_final: 0.7263 (mmm160) REVERT: A 317 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6854 (mm) REVERT: A 325 MET cc_start: 0.7966 (mtp) cc_final: 0.7643 (mtt) REVERT: A 425 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6141 (tm-30) REVERT: A 539 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7697 (mtp) REVERT: B 248 ARG cc_start: 0.8085 (tpt170) cc_final: 0.7249 (mmm160) REVERT: B 317 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6865 (mm) REVERT: B 425 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6264 (tm-30) REVERT: B 539 MET cc_start: 0.7970 (mtm) cc_final: 0.7698 (mtp) REVERT: C 239 MET cc_start: 0.7512 (mmm) cc_final: 0.7150 (mtm) REVERT: C 248 ARG cc_start: 0.8077 (tpt170) cc_final: 0.7239 (mmm160) REVERT: C 317 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6894 (mm) REVERT: C 425 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6244 (tm-30) REVERT: D 248 ARG cc_start: 0.8092 (tpt170) cc_final: 0.7251 (mmm160) REVERT: D 317 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6878 (mm) REVERT: D 425 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6261 (tm-30) outliers start: 31 outliers final: 16 residues processed: 166 average time/residue: 0.5691 time to fit residues: 106.6516 Evaluate side-chains 167 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU 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 A residue 539 MET Chi-restraints excluded: chain B residue 50 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 190 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 186 optimal weight: 0.0980 chunk 96 optimal weight: 5.9990 chunk 35 optimal weight: 0.0000 chunk 166 optimal weight: 0.5980 chunk 191 optimal weight: 0.7980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.150271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112198 restraints weight = 21842.989| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.88 r_work: 0.3328 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18248 Z= 0.101 Angle : 0.486 6.002 24780 Z= 0.246 Chirality : 0.040 0.244 2732 Planarity : 0.003 0.024 3164 Dihedral : 6.770 53.923 2908 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.77 % Allowed : 11.62 % Favored : 86.62 % 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: 1.16 (0.18), residues: 2196 helix: 1.70 (0.16), residues: 1060 sheet: -0.13 (0.39), residues: 184 loop : -0.02 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.013 0.001 TYR D 187 PHE 0.018 0.001 PHE D 263 TRP 0.007 0.001 TRP A 558 HIS 0.002 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00240 (18248) covalent geometry : angle 0.48603 (24780) hydrogen bonds : bond 0.03172 ( 752) hydrogen bonds : angle 4.17605 ( 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 177 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.685 Fit side-chains REVERT: A 239 MET cc_start: 0.7483 (mmm) cc_final: 0.7142 (mtm) REVERT: A 248 ARG cc_start: 0.8083 (tpt170) cc_final: 0.7247 (mmm160) REVERT: A 317 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6893 (mm) REVERT: A 325 MET cc_start: 0.7984 (mtp) cc_final: 0.7682 (mtt) REVERT: A 405 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7742 (mtt90) REVERT: A 425 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6216 (tm-30) REVERT: A 539 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7678 (mtp) REVERT: B 248 ARG cc_start: 0.8061 (tpt170) cc_final: 0.7242 (mmm160) REVERT: B 317 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6879 (mm) REVERT: B 325 MET cc_start: 0.7958 (mtp) cc_final: 0.7633 (mtt) REVERT: B 405 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7718 (mtt90) REVERT: B 425 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6293 (tm-30) REVERT: B 539 MET cc_start: 0.7941 (mtm) cc_final: 0.7690 (mtp) REVERT: C 239 MET cc_start: 0.7491 (mmm) cc_final: 0.7149 (mtm) REVERT: C 248 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7236 (mmm160) REVERT: C 317 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6871 (mm) REVERT: C 325 MET cc_start: 0.7963 (mtp) cc_final: 0.7632 (mtt) REVERT: C 405 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7723 (mtt90) REVERT: C 425 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: D 248 ARG cc_start: 0.8073 (tpt170) cc_final: 0.7247 (mmm160) REVERT: D 317 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6866 (mm) REVERT: D 325 MET cc_start: 0.7954 (mtp) cc_final: 0.7629 (mtt) REVERT: D 405 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7706 (mtt90) REVERT: D 425 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6294 (tm-30) outliers start: 33 outliers final: 16 residues processed: 166 average time/residue: 0.5542 time to fit residues: 103.7159 Evaluate side-chains 166 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU 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 A residue 539 MET Chi-restraints excluded: chain B residue 50 LEU 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 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: 0.9980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 116 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.109860 restraints weight = 21720.611| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.81 r_work: 0.3308 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18248 Z= 0.116 Angle : 0.499 9.314 24780 Z= 0.251 Chirality : 0.041 0.278 2732 Planarity : 0.003 0.024 3164 Dihedral : 6.713 54.367 2908 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.34 % Allowed : 12.21 % Favored : 86.46 % 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: 1.14 (0.18), residues: 2196 helix: 1.68 (0.16), residues: 1060 sheet: -0.15 (0.39), residues: 184 loop : -0.03 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 67 TYR 0.013 0.001 TYR B 187 PHE 0.021 0.001 PHE D 263 TRP 0.006 0.001 TRP A 558 HIS 0.002 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00284 (18248) covalent geometry : angle 0.49860 (24780) hydrogen bonds : bond 0.03357 ( 752) hydrogen bonds : angle 4.24233 ( 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 169 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.670 Fit side-chains REVERT: A 248 ARG cc_start: 0.8086 (tpt170) cc_final: 0.7245 (mmm160) REVERT: A 317 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6892 (mm) REVERT: A 325 MET cc_start: 0.7990 (mtp) cc_final: 0.7689 (mtt) REVERT: A 405 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7788 (mtt90) REVERT: A 425 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: A 539 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7668 (mtp) REVERT: B 248 ARG cc_start: 0.8073 (tpt170) cc_final: 0.7241 (mmm160) REVERT: B 317 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6911 (mm) REVERT: B 405 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7740 (mtt90) REVERT: B 425 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6257 (tm-30) REVERT: B 539 MET cc_start: 0.7961 (mtm) cc_final: 0.7714 (mtp) REVERT: C 219 MET cc_start: 0.7766 (mtm) cc_final: 0.7565 (mtm) REVERT: C 248 ARG cc_start: 0.8073 (tpt170) cc_final: 0.7225 (mmm160) REVERT: C 317 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6961 (mm) REVERT: C 405 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7747 (mtt90) REVERT: C 425 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6264 (tm-30) REVERT: D 248 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7239 (mmm160) REVERT: D 317 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6898 (mm) REVERT: D 405 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7732 (mtt90) REVERT: D 425 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6262 (tm-30) outliers start: 25 outliers final: 16 residues processed: 160 average time/residue: 0.6018 time to fit residues: 108.5461 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 : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU 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 A residue 539 MET Chi-restraints excluded: chain B residue 50 LEU 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 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: 3.9990 chunk 218 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 152 optimal weight: 0.0070 chunk 135 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.148672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110287 restraints weight = 21976.876| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.83 r_work: 0.3312 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1956 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= 0.111 Angle : 0.496 9.473 24780 Z= 0.251 Chirality : 0.041 0.301 2732 Planarity : 0.003 0.024 3164 Dihedral : 6.646 54.114 2908 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.55 % Allowed : 12.15 % Favored : 86.30 % 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: 1.13 (0.18), residues: 2196 helix: 1.69 (0.16), residues: 1060 sheet: -0.18 (0.39), residues: 184 loop : -0.06 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.014 0.001 TYR D 187 PHE 0.018 0.001 PHE D 471 TRP 0.007 0.001 TRP C 342 HIS 0.002 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00269 (18248) covalent geometry : angle 0.49622 (24780) hydrogen bonds : bond 0.03299 ( 752) hydrogen bonds : angle 4.22757 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4258.43 seconds wall clock time: 74 minutes 9.89 seconds (4449.89 seconds total)