Starting phenix.real_space_refine on Thu Mar 5 01:48:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xdf_33146/03_2026/7xdf_33146.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xdf_33146/03_2026/7xdf_33146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xdf_33146/03_2026/7xdf_33146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xdf_33146/03_2026/7xdf_33146.map" model { file = "/net/cci-nas-00/data/ceres_data/7xdf_33146/03_2026/7xdf_33146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xdf_33146/03_2026/7xdf_33146.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 92 5.16 5 C 11396 2.51 5 N 3020 2.21 5 O 3344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s 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: 17868 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "B" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "C" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "D" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'JBR': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.79, per 1000 atoms: 0.21 Number of scatterers: 17868 At special positions: 0 Unit cell: (77.9, 133.66, 133.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 16 15.00 O 3344 8.00 N 3020 7.00 C 11396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 803.3 milliseconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4088 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 8 sheets defined 54.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.664A pdb=" N MET A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.609A pdb=" N PHE A 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 60 through 75 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.593A pdb=" N GLU A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 103 Processing helix chain 'A' and resid 103 through 112 Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.543A pdb=" N LEU A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.816A pdb=" N VAL A 181 " --> pdb=" O MET A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.572A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 247 removed outlier: 4.080A pdb=" N ASP A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 281 through 298 removed outlier: 3.598A pdb=" N LYS A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.618A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.526A pdb=" N ASN A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 466 through 469 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 487 through 501 removed outlier: 4.297A pdb=" N PHE A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 518 through 537 Processing helix chain 'A' and resid 548 through 557 removed outlier: 3.569A pdb=" N ARG A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.663A pdb=" N MET B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.609A pdb=" N PHE B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 60 through 75 Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.594A pdb=" N GLU B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 103 through 112 Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.543A pdb=" N LEU B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 148 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.816A pdb=" N VAL B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.573A pdb=" N LEU B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 247 removed outlier: 4.079A pdb=" N ASP B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.597A pdb=" N LYS B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 330 Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.617A pdb=" N LYS B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 400 through 411 removed outlier: 3.526A pdb=" N ASN B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 466 through 469 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 487 through 501 removed outlier: 4.297A pdb=" N PHE B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 548 through 557 removed outlier: 3.568A pdb=" N ARG B 556 " --> pdb=" O TYR B 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.664A pdb=" N MET C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.608A pdb=" N PHE C 40 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 60 through 75 Processing helix chain 'C' and resid 77 through 92 removed outlier: 3.593A pdb=" N GLU C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 Processing helix chain 'C' and resid 103 through 112 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.543A pdb=" N LEU C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.816A pdb=" N VAL C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.573A pdb=" N LEU C 213 " --> pdb=" O ASN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 247 removed outlier: 4.079A pdb=" N ASP C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 270 Processing helix chain 'C' and resid 281 through 298 removed outlier: 3.598A pdb=" N LYS C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 Processing helix chain 'C' and resid 333 through 339 removed outlier: 3.618A pdb=" N LYS C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 400 through 411 removed outlier: 3.526A pdb=" N ASN C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 466 through 469 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 487 through 501 removed outlier: 4.297A pdb=" N PHE C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 518 through 537 Processing helix chain 'C' and resid 548 through 557 removed outlier: 3.569A pdb=" N ARG C 556 " --> pdb=" O TYR C 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 31 removed outlier: 3.665A pdb=" N MET D 29 " --> pdb=" O GLY D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.609A pdb=" N PHE D 40 " --> pdb=" O GLY D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 60 through 75 Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.594A pdb=" N GLU D 90 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 103 Processing helix chain 'D' and resid 103 through 112 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 114 through 124 removed outlier: 3.543A pdb=" N LEU D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 148 Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.817A pdb=" N VAL D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.572A pdb=" N LEU D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 247 removed outlier: 4.079A pdb=" N ASP D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 270 Processing helix chain 'D' and resid 281 through 298 removed outlier: 3.597A pdb=" N LYS D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 330 Processing helix chain 'D' and resid 333 through 339 removed outlier: 3.617A pdb=" N LYS D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 400 through 411 removed outlier: 3.526A pdb=" N ASN D 411 " --> pdb=" O MET D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 Processing helix chain 'D' and resid 466 through 469 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 487 through 501 removed outlier: 4.296A pdb=" N PHE D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 510 Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 518 through 537 Processing helix chain 'D' and resid 548 through 557 removed outlier: 3.567A pdb=" N ARG D 556 " --> pdb=" O TYR D 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 136 removed outlier: 6.189A pdb=" N LEU A 133 " --> pdb=" O CYS A 202 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP A 204 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 135 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 157 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 201 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 159 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE A 203 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR A 161 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 158 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU A 255 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL A 160 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE A 307 " --> pdb=" O TRP A 342 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE A 344 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE A 309 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.188A pdb=" N LEU B 133 " --> pdb=" O CYS B 202 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP B 204 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 135 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA B 157 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL B 201 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 159 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE B 203 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR B 161 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 158 " --> pdb=" O GLN B 253 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU B 255 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL B 160 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE B 307 " --> pdb=" O TRP B 342 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE B 344 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE B 309 " --> pdb=" O PHE B 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.189A pdb=" N LEU C 133 " --> pdb=" O CYS C 202 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP C 204 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 135 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA C 157 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL C 201 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 159 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE C 203 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR C 161 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 158 " --> pdb=" O GLN C 253 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU C 255 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL C 160 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE C 307 " --> pdb=" O TRP C 342 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE C 344 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE C 309 " --> pdb=" O PHE C 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 136 removed outlier: 6.188A pdb=" N LEU D 133 " --> pdb=" O CYS D 202 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP D 204 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE D 135 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA D 157 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL D 201 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL D 159 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE D 203 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR D 161 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 158 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU D 255 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL D 160 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.405A pdb=" N ILE D 307 " --> pdb=" O TRP D 342 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE D 344 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE D 309 " --> pdb=" O PHE D 344 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2948 1.31 - 1.43: 4782 1.43 - 1.56: 10338 1.56 - 1.68: 72 1.68 - 1.81: 148 Bond restraints: 18288 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.230 0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C2D NAD C 601 " pdb=" C3D NAD C 601 " ideal model delta sigma weight residual 1.531 1.231 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C2D NAD B 601 " pdb=" C3D NAD B 601 " ideal model delta sigma weight residual 1.531 1.231 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C2D NAD D 601 " pdb=" C3D NAD D 601 " ideal model delta sigma weight residual 1.531 1.231 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C2D NAD C 602 " pdb=" C3D NAD C 602 " ideal model delta sigma weight residual 1.531 1.237 0.294 2.00e-02 2.50e+03 2.16e+02 ... (remaining 18283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 24339 2.68 - 5.36: 391 5.36 - 8.03: 66 8.03 - 10.71: 32 10.71 - 13.39: 16 Bond angle restraints: 24844 Sorted by residual: angle pdb=" O1A NAD B 602 " pdb=" PA NAD B 602 " pdb=" O2A NAD B 602 " ideal model delta sigma weight residual 122.64 109.25 13.39 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O1A NAD C 602 " pdb=" PA NAD C 602 " pdb=" O2A NAD C 602 " ideal model delta sigma weight residual 122.64 109.26 13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O1A NAD B 601 " pdb=" PA NAD B 601 " pdb=" O2A NAD B 601 " ideal model delta sigma weight residual 122.64 109.28 13.36 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.29 13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O1A NAD C 601 " pdb=" PA NAD C 601 " pdb=" O2A NAD C 601 " ideal model delta sigma weight residual 122.64 109.29 13.35 3.00e+00 1.11e-01 1.98e+01 ... (remaining 24839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 10040 17.13 - 34.27: 976 34.27 - 51.40: 157 51.40 - 68.53: 69 68.53 - 85.67: 38 Dihedral angle restraints: 11280 sinusoidal: 4896 harmonic: 6384 Sorted by residual: dihedral pdb=" CA GLU C 304 " pdb=" C GLU C 304 " pdb=" N HIS C 305 " pdb=" CA HIS C 305 " ideal model delta harmonic sigma weight residual 180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU B 304 " pdb=" C GLU B 304 " pdb=" N HIS B 305 " pdb=" CA HIS B 305 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU A 304 " pdb=" C GLU A 304 " pdb=" N HIS A 305 " pdb=" CA HIS A 305 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 11277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2445 0.075 - 0.151: 257 0.151 - 0.226: 22 0.226 - 0.302: 4 0.302 - 0.377: 4 Chirality restraints: 2732 Sorted by residual: chirality pdb=" C4D NAD B 601 " pdb=" C3D NAD B 601 " pdb=" C5D NAD B 601 " pdb=" O4D NAD B 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C4D NAD C 601 " pdb=" C3D NAD C 601 " pdb=" C5D NAD C 601 " pdb=" O4D NAD C 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C4D NAD A 601 " pdb=" C3D NAD A 601 " pdb=" C5D NAD A 601 " pdb=" O4D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 2729 not shown) Planarity restraints: 3164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 26 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO B 27 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 26 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO C 27 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 26 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 27 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.027 5.00e-02 4.00e+02 ... (remaining 3161 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 250 2.63 - 3.20: 16531 3.20 - 3.77: 28042 3.77 - 4.33: 40932 4.33 - 4.90: 67949 Nonbonded interactions: 153704 Sorted by model distance: nonbonded pdb=" OD1 ASP A 236 " pdb=" OH TYR A 269 " model vdw 2.065 3.040 nonbonded pdb=" OD1 ASP C 236 " pdb=" OH TYR C 269 " model vdw 2.065 3.040 nonbonded pdb=" OD1 ASP B 236 " pdb=" OH TYR B 269 " model vdw 2.066 3.040 nonbonded pdb=" OD1 ASP D 236 " pdb=" OH TYR D 269 " model vdw 2.066 3.040 nonbonded pdb=" OE2 GLU B 59 " pdb=" NH2 ARG B 67 " model vdw 2.089 3.120 ... (remaining 153699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 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: 3.800 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.780 Find NCS groups from input model: 0.140 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.342 18304 Z= 0.926 Angle : 0.929 13.390 24844 Z= 0.432 Chirality : 0.049 0.377 2732 Planarity : 0.006 0.048 3164 Dihedral : 14.801 85.667 7192 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2196 helix: 0.35 (0.16), residues: 1036 sheet: 1.03 (0.36), residues: 204 loop : -0.02 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 405 TYR 0.013 0.001 TYR B 562 PHE 0.023 0.002 PHE D 471 TRP 0.009 0.001 TRP A 558 HIS 0.007 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.01397 (18288) covalent geometry : angle 0.92930 (24844) hydrogen bonds : bond 0.17628 ( 748) hydrogen bonds : angle 6.96088 ( 2184) Misc. bond : bond 0.20771 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.706 Fit side-chains REVERT: A 152 GLU cc_start: 0.7477 (mp0) cc_final: 0.7190 (tp30) REVERT: A 314 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6767 (mm-30) REVERT: A 334 GLU cc_start: 0.7586 (tt0) cc_final: 0.7342 (tt0) REVERT: A 352 LYS cc_start: 0.5859 (mmpt) cc_final: 0.4650 (pttt) REVERT: A 359 ASP cc_start: 0.7526 (m-30) cc_final: 0.7264 (m-30) REVERT: A 398 LEU cc_start: 0.7420 (mm) cc_final: 0.7190 (mm) REVERT: A 460 PHE cc_start: 0.7819 (m-80) cc_final: 0.7421 (m-80) REVERT: A 488 ASP cc_start: 0.7397 (m-30) cc_final: 0.6964 (m-30) REVERT: A 565 LEU cc_start: 0.9033 (mt) cc_final: 0.8826 (mt) REVERT: B 29 MET cc_start: 0.8452 (mtp) cc_final: 0.8226 (mtp) REVERT: B 152 GLU cc_start: 0.7508 (mp0) cc_final: 0.7229 (tp30) REVERT: B 352 LYS cc_start: 0.5974 (mmpt) cc_final: 0.4766 (pttt) REVERT: B 359 ASP cc_start: 0.7523 (m-30) cc_final: 0.7279 (m-30) REVERT: B 460 PHE cc_start: 0.7770 (m-80) cc_final: 0.7390 (m-80) REVERT: B 488 ASP cc_start: 0.7374 (m-30) cc_final: 0.6958 (m-30) REVERT: C 29 MET cc_start: 0.8447 (mtp) cc_final: 0.8219 (mtp) REVERT: C 152 GLU cc_start: 0.7519 (mp0) cc_final: 0.7222 (tp30) REVERT: C 210 ILE cc_start: 0.8340 (pt) cc_final: 0.8138 (tp) REVERT: C 314 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6718 (mm-30) REVERT: C 352 LYS cc_start: 0.5933 (mmpt) cc_final: 0.4692 (pttt) REVERT: C 359 ASP cc_start: 0.7511 (m-30) cc_final: 0.7248 (m-30) REVERT: C 398 LEU cc_start: 0.7400 (mm) cc_final: 0.7180 (mm) REVERT: C 460 PHE cc_start: 0.7804 (m-80) cc_final: 0.7423 (m-80) REVERT: C 488 ASP cc_start: 0.7375 (m-30) cc_final: 0.6959 (m-30) REVERT: C 565 LEU cc_start: 0.9038 (mt) cc_final: 0.8835 (mt) REVERT: D 29 MET cc_start: 0.8408 (mtp) cc_final: 0.8176 (mtp) REVERT: D 152 GLU cc_start: 0.7472 (mp0) cc_final: 0.7205 (tp30) REVERT: D 314 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6758 (mm-30) REVERT: D 334 GLU cc_start: 0.7582 (tt0) cc_final: 0.7337 (tt0) REVERT: D 352 LYS cc_start: 0.5939 (mmpt) cc_final: 0.4717 (pttt) REVERT: D 359 ASP cc_start: 0.7539 (m-30) cc_final: 0.7291 (m-30) REVERT: D 398 LEU cc_start: 0.7419 (mm) cc_final: 0.7210 (mm) REVERT: D 460 PHE cc_start: 0.7805 (m-80) cc_final: 0.7400 (m-80) REVERT: D 488 ASP cc_start: 0.7377 (m-30) cc_final: 0.6948 (m-30) REVERT: D 565 LEU cc_start: 0.9039 (mt) cc_final: 0.8830 (mt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.6658 time to fit residues: 249.3822 Evaluate side-chains 229 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.0050 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 509 GLN B 61 GLN B 425 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 425 GLN D 509 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105206 restraints weight = 20955.925| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.86 r_work: 0.3146 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18304 Z= 0.172 Angle : 0.608 6.252 24844 Z= 0.312 Chirality : 0.045 0.203 2732 Planarity : 0.005 0.045 3164 Dihedral : 11.273 59.296 2908 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.39 % Allowed : 9.53 % Favored : 89.08 % 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: 0.81 (0.18), residues: 2196 helix: 0.93 (0.16), residues: 1056 sheet: 0.82 (0.34), residues: 204 loop : 0.18 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 270 TYR 0.011 0.001 TYR B 469 PHE 0.028 0.002 PHE B 471 TRP 0.010 0.001 TRP A 558 HIS 0.007 0.002 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00406 (18288) covalent geometry : angle 0.60787 (24844) hydrogen bonds : bond 0.05368 ( 748) hydrogen bonds : angle 5.06388 ( 2184) Misc. bond : bond 0.00105 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.695 Fit side-chains REVERT: A 118 LEU cc_start: 0.8319 (tp) cc_final: 0.7980 (mt) REVERT: A 152 GLU cc_start: 0.8203 (mp0) cc_final: 0.7527 (mm-30) REVERT: A 314 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6957 (mm-30) REVERT: A 352 LYS cc_start: 0.5970 (mmpt) cc_final: 0.4729 (pttt) REVERT: A 359 ASP cc_start: 0.7701 (m-30) cc_final: 0.7428 (m-30) REVERT: A 460 PHE cc_start: 0.8010 (m-80) cc_final: 0.7625 (m-80) REVERT: B 118 LEU cc_start: 0.8276 (tp) cc_final: 0.8021 (tp) REVERT: B 152 GLU cc_start: 0.8276 (mp0) cc_final: 0.7606 (mm-30) REVERT: B 352 LYS cc_start: 0.6103 (mmpt) cc_final: 0.4828 (pttt) REVERT: B 359 ASP cc_start: 0.7795 (m-30) cc_final: 0.7561 (m-30) REVERT: B 460 PHE cc_start: 0.8027 (m-80) cc_final: 0.7612 (m-80) REVERT: C 152 GLU cc_start: 0.8280 (mp0) cc_final: 0.7601 (mm-30) REVERT: C 210 ILE cc_start: 0.8252 (pt) cc_final: 0.7952 (tp) REVERT: C 314 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6893 (mm-30) REVERT: C 352 LYS cc_start: 0.6004 (mmpt) cc_final: 0.4733 (pttt) REVERT: C 359 ASP cc_start: 0.7779 (m-30) cc_final: 0.7530 (m-30) REVERT: C 385 LYS cc_start: 0.8597 (mppt) cc_final: 0.8395 (mmtt) REVERT: C 460 PHE cc_start: 0.8011 (m-80) cc_final: 0.7576 (m-80) REVERT: D 118 LEU cc_start: 0.8322 (tp) cc_final: 0.7987 (mt) REVERT: D 152 GLU cc_start: 0.8231 (mp0) cc_final: 0.7546 (mm-30) REVERT: D 314 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6973 (mm-30) REVERT: D 334 GLU cc_start: 0.7946 (tt0) cc_final: 0.7713 (tt0) REVERT: D 352 LYS cc_start: 0.5933 (mmpt) cc_final: 0.4709 (pttt) REVERT: D 359 ASP cc_start: 0.7768 (m-30) cc_final: 0.7444 (m-30) REVERT: D 363 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7128 (tm-30) REVERT: D 385 LYS cc_start: 0.8583 (mppt) cc_final: 0.8380 (mmtt) REVERT: D 460 PHE cc_start: 0.8021 (m-80) cc_final: 0.7630 (m-80) outliers start: 26 outliers final: 4 residues processed: 241 average time/residue: 0.6764 time to fit residues: 179.9780 Evaluate side-chains 199 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 195 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 438 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 137 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 61 GLN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104771 restraints weight = 20649.636| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.89 r_work: 0.3116 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18304 Z= 0.146 Angle : 0.563 6.132 24844 Z= 0.286 Chirality : 0.044 0.197 2732 Planarity : 0.005 0.043 3164 Dihedral : 9.305 57.601 2908 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.39 % Allowed : 11.88 % Favored : 86.72 % 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: 0.89 (0.18), residues: 2196 helix: 1.05 (0.16), residues: 1060 sheet: 0.55 (0.32), residues: 204 loop : 0.22 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.010 0.001 TYR C 469 PHE 0.025 0.002 PHE D 471 TRP 0.009 0.001 TRP A 558 HIS 0.006 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00347 (18288) covalent geometry : angle 0.56341 (24844) hydrogen bonds : bond 0.04358 ( 748) hydrogen bonds : angle 4.70851 ( 2184) Misc. bond : bond 0.00172 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8133 (tp) cc_final: 0.7833 (mt) REVERT: A 152 GLU cc_start: 0.8142 (mp0) cc_final: 0.7367 (mm-30) REVERT: A 352 LYS cc_start: 0.5937 (mmpt) cc_final: 0.4682 (pttt) REVERT: A 359 ASP cc_start: 0.7710 (m-30) cc_final: 0.7374 (m-30) REVERT: A 460 PHE cc_start: 0.7930 (m-80) cc_final: 0.7503 (m-80) REVERT: B 118 LEU cc_start: 0.8153 (tp) cc_final: 0.7873 (mt) REVERT: B 152 GLU cc_start: 0.8190 (mp0) cc_final: 0.7395 (mm-30) REVERT: B 335 GLN cc_start: 0.7379 (tp40) cc_final: 0.6902 (mp10) REVERT: B 352 LYS cc_start: 0.5974 (mmpt) cc_final: 0.4708 (pttt) REVERT: B 359 ASP cc_start: 0.7729 (m-30) cc_final: 0.7415 (m-30) REVERT: B 460 PHE cc_start: 0.7983 (m-80) cc_final: 0.7585 (m-80) REVERT: C 152 GLU cc_start: 0.8190 (mp0) cc_final: 0.7392 (mm-30) REVERT: C 210 ILE cc_start: 0.8206 (pt) cc_final: 0.7901 (tp) REVERT: C 335 GLN cc_start: 0.7364 (tp40) cc_final: 0.6894 (mp10) REVERT: C 352 LYS cc_start: 0.5956 (mmpt) cc_final: 0.4684 (pttt) REVERT: C 359 ASP cc_start: 0.7698 (m-30) cc_final: 0.7359 (m-30) REVERT: C 460 PHE cc_start: 0.7929 (m-80) cc_final: 0.7514 (m-80) REVERT: D 118 LEU cc_start: 0.8120 (tp) cc_final: 0.7816 (mt) REVERT: D 152 GLU cc_start: 0.8162 (mp0) cc_final: 0.7390 (mm-30) REVERT: D 334 GLU cc_start: 0.7814 (tt0) cc_final: 0.7601 (tt0) REVERT: D 335 GLN cc_start: 0.7349 (tp40) cc_final: 0.6939 (mp10) REVERT: D 352 LYS cc_start: 0.5841 (mmpt) cc_final: 0.4623 (pttt) REVERT: D 359 ASP cc_start: 0.7683 (m-30) cc_final: 0.7323 (m-30) REVERT: D 460 PHE cc_start: 0.7949 (m-80) cc_final: 0.7526 (m-80) outliers start: 26 outliers final: 6 residues processed: 231 average time/residue: 0.6474 time to fit residues: 166.0504 Evaluate side-chains 193 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain D residue 145 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 149 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104490 restraints weight = 20573.092| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.88 r_work: 0.3128 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18304 Z= 0.147 Angle : 0.552 6.154 24844 Z= 0.281 Chirality : 0.044 0.206 2732 Planarity : 0.004 0.042 3164 Dihedral : 8.733 59.140 2908 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.94 % Allowed : 11.67 % Favored : 85.39 % 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: 0.81 (0.18), residues: 2196 helix: 1.08 (0.16), residues: 1072 sheet: -0.02 (0.28), residues: 256 loop : 0.21 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 227 TYR 0.009 0.001 TYR B 469 PHE 0.025 0.002 PHE B 471 TRP 0.009 0.001 TRP C 558 HIS 0.006 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00353 (18288) covalent geometry : angle 0.55227 (24844) hydrogen bonds : bond 0.04095 ( 748) hydrogen bonds : angle 4.53248 ( 2184) Misc. bond : bond 0.00128 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8028 (mt) REVERT: A 352 LYS cc_start: 0.5933 (mmpt) cc_final: 0.4714 (pttt) REVERT: A 359 ASP cc_start: 0.7685 (m-30) cc_final: 0.7365 (m-30) REVERT: A 432 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6721 (mt-10) REVERT: A 460 PHE cc_start: 0.7951 (m-80) cc_final: 0.7750 (m-80) REVERT: B 118 LEU cc_start: 0.8175 (tp) cc_final: 0.7886 (mt) REVERT: B 335 GLN cc_start: 0.7305 (tp40) cc_final: 0.6813 (mp10) REVERT: B 336 GLU cc_start: 0.7279 (tp30) cc_final: 0.7073 (tp30) REVERT: B 352 LYS cc_start: 0.5982 (mmpt) cc_final: 0.4709 (pttt) REVERT: B 359 ASP cc_start: 0.7679 (m-30) cc_final: 0.7372 (m-30) REVERT: B 460 PHE cc_start: 0.7931 (m-80) cc_final: 0.7478 (m-80) REVERT: C 210 ILE cc_start: 0.8195 (pt) cc_final: 0.7893 (tp) REVERT: C 352 LYS cc_start: 0.5921 (mmpt) cc_final: 0.4691 (pttt) REVERT: C 359 ASP cc_start: 0.7666 (m-30) cc_final: 0.7344 (m-30) REVERT: C 460 PHE cc_start: 0.7959 (m-80) cc_final: 0.7547 (m-80) REVERT: D 334 GLU cc_start: 0.7770 (tt0) cc_final: 0.7569 (tt0) REVERT: D 335 GLN cc_start: 0.7265 (tp40) cc_final: 0.6827 (mp10) REVERT: D 352 LYS cc_start: 0.5863 (mmpt) cc_final: 0.4637 (pttt) REVERT: D 359 ASP cc_start: 0.7677 (m-30) cc_final: 0.7350 (m-30) outliers start: 55 outliers final: 18 residues processed: 245 average time/residue: 0.6643 time to fit residues: 180.8637 Evaluate side-chains 199 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 8 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 0.0670 chunk 180 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106534 restraints weight = 20904.063| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.88 r_work: 0.3157 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18304 Z= 0.115 Angle : 0.524 6.077 24844 Z= 0.265 Chirality : 0.043 0.210 2732 Planarity : 0.004 0.050 3164 Dihedral : 8.839 59.395 2908 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.98 % Allowed : 13.54 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2196 helix: 1.26 (0.16), residues: 1072 sheet: 0.04 (0.28), residues: 256 loop : 0.20 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.007 0.001 TYR C 112 PHE 0.028 0.002 PHE D 471 TRP 0.009 0.001 TRP B 558 HIS 0.005 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00264 (18288) covalent geometry : angle 0.52414 (24844) hydrogen bonds : bond 0.03654 ( 748) hydrogen bonds : angle 4.39638 ( 2184) Misc. bond : bond 0.00172 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 352 LYS cc_start: 0.6048 (mmpt) cc_final: 0.4801 (pttt) REVERT: A 359 ASP cc_start: 0.7700 (m-30) cc_final: 0.7407 (m-30) REVERT: A 432 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6809 (mt-10) REVERT: A 460 PHE cc_start: 0.8011 (m-80) cc_final: 0.7603 (m-80) REVERT: B 118 LEU cc_start: 0.8363 (tp) cc_final: 0.8120 (mt) REVERT: B 335 GLN cc_start: 0.7246 (tp40) cc_final: 0.6777 (mp10) REVERT: B 336 GLU cc_start: 0.7358 (tp30) cc_final: 0.7080 (tp30) REVERT: B 352 LYS cc_start: 0.6097 (mmpt) cc_final: 0.4830 (pttt) REVERT: B 359 ASP cc_start: 0.7723 (m-30) cc_final: 0.7458 (m-30) REVERT: B 432 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6814 (mt-10) REVERT: B 460 PHE cc_start: 0.8040 (m-80) cc_final: 0.7610 (m-80) REVERT: B 501 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.6483 (mp10) REVERT: C 210 ILE cc_start: 0.8206 (pt) cc_final: 0.7921 (tp) REVERT: C 336 GLU cc_start: 0.7294 (tp30) cc_final: 0.7078 (tp30) REVERT: C 352 LYS cc_start: 0.6083 (mmpt) cc_final: 0.4814 (pttt) REVERT: C 359 ASP cc_start: 0.7699 (m-30) cc_final: 0.7416 (m-30) REVERT: C 432 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6804 (mt-10) REVERT: C 460 PHE cc_start: 0.8029 (m-80) cc_final: 0.7645 (m-80) REVERT: C 501 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: D 334 GLU cc_start: 0.7857 (tt0) cc_final: 0.7631 (tt0) REVERT: D 335 GLN cc_start: 0.7271 (tp40) cc_final: 0.6832 (mp10) REVERT: D 336 GLU cc_start: 0.7264 (tp30) cc_final: 0.7062 (tp30) REVERT: D 352 LYS cc_start: 0.5973 (mmpt) cc_final: 0.4718 (pptt) REVERT: D 359 ASP cc_start: 0.7744 (m-30) cc_final: 0.7440 (m-30) REVERT: D 432 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6800 (mt-10) outliers start: 37 outliers final: 14 residues processed: 225 average time/residue: 0.6637 time to fit residues: 165.3526 Evaluate side-chains 202 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 101 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN C 281 GLN D 281 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103249 restraints weight = 20870.060| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.87 r_work: 0.3108 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18304 Z= 0.194 Angle : 0.572 6.298 24844 Z= 0.291 Chirality : 0.046 0.225 2732 Planarity : 0.005 0.045 3164 Dihedral : 8.789 59.277 2908 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.94 % Allowed : 13.01 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2196 helix: 1.12 (0.16), residues: 1076 sheet: -0.06 (0.28), residues: 256 loop : 0.09 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 197 TYR 0.012 0.001 TYR A 97 PHE 0.028 0.002 PHE D 471 TRP 0.010 0.001 TRP A 558 HIS 0.006 0.002 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00479 (18288) covalent geometry : angle 0.57231 (24844) hydrogen bonds : bond 0.04341 ( 748) hydrogen bonds : angle 4.54110 ( 2184) Misc. bond : bond 0.00120 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8138 (mt) REVERT: A 179 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8066 (mm) REVERT: A 352 LYS cc_start: 0.6080 (mmpt) cc_final: 0.4823 (pptt) REVERT: A 359 ASP cc_start: 0.7782 (m-30) cc_final: 0.7505 (m-30) REVERT: A 432 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6840 (mt-10) REVERT: A 438 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6159 (pm20) REVERT: A 501 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: B 118 LEU cc_start: 0.8425 (tp) cc_final: 0.8189 (mt) REVERT: B 335 GLN cc_start: 0.7403 (tp40) cc_final: 0.6860 (mp10) REVERT: B 336 GLU cc_start: 0.7379 (tp30) cc_final: 0.7035 (tp30) REVERT: B 352 LYS cc_start: 0.6097 (mmpt) cc_final: 0.4819 (pptt) REVERT: B 359 ASP cc_start: 0.7818 (m-30) cc_final: 0.7561 (m-30) REVERT: B 432 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6780 (mt-10) REVERT: B 501 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.6703 (mp10) REVERT: C 210 ILE cc_start: 0.8250 (pt) cc_final: 0.7939 (tp) REVERT: C 336 GLU cc_start: 0.7388 (tp30) cc_final: 0.7160 (tp30) REVERT: C 352 LYS cc_start: 0.6085 (mmpt) cc_final: 0.4804 (pptt) REVERT: C 359 ASP cc_start: 0.7815 (m-30) cc_final: 0.7544 (m-30) REVERT: C 432 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6773 (mt-10) REVERT: C 438 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6148 (pm20) REVERT: C 501 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.6744 (mp10) REVERT: D 334 GLU cc_start: 0.7860 (tt0) cc_final: 0.7643 (tt0) REVERT: D 335 GLN cc_start: 0.7314 (tp40) cc_final: 0.6808 (mp10) REVERT: D 336 GLU cc_start: 0.7314 (tp30) cc_final: 0.7020 (tp30) REVERT: D 352 LYS cc_start: 0.6058 (mmpt) cc_final: 0.4760 (pttt) REVERT: D 359 ASP cc_start: 0.7840 (m-30) cc_final: 0.7532 (m-30) REVERT: D 432 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6786 (mt-10) REVERT: D 501 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.6769 (mp10) outliers start: 55 outliers final: 20 residues processed: 234 average time/residue: 0.6622 time to fit residues: 171.2986 Evaluate side-chains 211 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 110 optimal weight: 0.8980 chunk 208 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 104 optimal weight: 0.0470 chunk 184 optimal weight: 0.2980 chunk 201 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104888 restraints weight = 21010.305| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.89 r_work: 0.3128 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18304 Z= 0.138 Angle : 0.541 6.155 24844 Z= 0.274 Chirality : 0.044 0.219 2732 Planarity : 0.004 0.040 3164 Dihedral : 8.433 58.614 2908 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.09 % Allowed : 14.19 % Favored : 83.73 % 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: 0.89 (0.18), residues: 2196 helix: 1.25 (0.16), residues: 1072 sheet: -0.09 (0.28), residues: 256 loop : 0.12 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 197 TYR 0.009 0.001 TYR C 112 PHE 0.027 0.002 PHE D 471 TRP 0.009 0.001 TRP B 558 HIS 0.006 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00329 (18288) covalent geometry : angle 0.54109 (24844) hydrogen bonds : bond 0.03891 ( 748) hydrogen bonds : angle 4.45299 ( 2184) Misc. bond : bond 0.00119 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8152 (mt) REVERT: A 339 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7781 (mmmm) REVERT: A 352 LYS cc_start: 0.6146 (mmpt) cc_final: 0.4908 (pptt) REVERT: A 359 ASP cc_start: 0.7786 (m-30) cc_final: 0.7516 (m-30) REVERT: A 432 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6810 (mt-10) REVERT: A 438 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6123 (pm20) REVERT: A 501 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.6561 (mp10) REVERT: B 118 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8212 (mt) REVERT: B 335 GLN cc_start: 0.7359 (tp40) cc_final: 0.7134 (pp30) REVERT: B 336 GLU cc_start: 0.7362 (tp30) cc_final: 0.7049 (tp30) REVERT: B 352 LYS cc_start: 0.6211 (mmpt) cc_final: 0.4954 (pptt) REVERT: B 359 ASP cc_start: 0.7808 (m-30) cc_final: 0.7559 (m-30) REVERT: B 432 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6811 (mt-10) REVERT: B 438 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6400 (pt0) REVERT: B 501 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: C 47 MET cc_start: 0.8869 (ptp) cc_final: 0.8654 (ptp) REVERT: C 210 ILE cc_start: 0.8239 (pt) cc_final: 0.7948 (tp) REVERT: C 336 GLU cc_start: 0.7368 (tp30) cc_final: 0.7125 (tp30) REVERT: C 352 LYS cc_start: 0.6199 (mmpt) cc_final: 0.4937 (pptt) REVERT: C 359 ASP cc_start: 0.7814 (m-30) cc_final: 0.7554 (m-30) REVERT: C 438 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: C 501 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.6662 (mp10) REVERT: D 334 GLU cc_start: 0.7856 (tt0) cc_final: 0.7651 (tt0) REVERT: D 335 GLN cc_start: 0.7303 (tp40) cc_final: 0.6798 (mp10) REVERT: D 336 GLU cc_start: 0.7310 (tp30) cc_final: 0.6978 (tp30) REVERT: D 352 LYS cc_start: 0.6040 (mmpt) cc_final: 0.4771 (pttt) REVERT: D 359 ASP cc_start: 0.7834 (m-30) cc_final: 0.7536 (m-30) REVERT: D 432 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6773 (mt-10) REVERT: D 438 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6360 (pt0) REVERT: D 501 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.6542 (mp10) outliers start: 39 outliers final: 16 residues processed: 223 average time/residue: 0.6679 time to fit residues: 164.7236 Evaluate side-chains 209 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 123 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 159 optimal weight: 0.2980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104569 restraints weight = 21009.149| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.89 r_work: 0.3130 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18304 Z= 0.148 Angle : 0.550 6.250 24844 Z= 0.277 Chirality : 0.044 0.246 2732 Planarity : 0.004 0.039 3164 Dihedral : 8.520 57.333 2908 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.36 % Allowed : 14.19 % Favored : 83.46 % 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: 0.87 (0.17), residues: 2196 helix: 1.25 (0.16), residues: 1072 sheet: -0.10 (0.28), residues: 256 loop : 0.09 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.009 0.001 TYR B 97 PHE 0.027 0.002 PHE D 471 TRP 0.009 0.001 TRP C 558 HIS 0.006 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00358 (18288) covalent geometry : angle 0.55024 (24844) hydrogen bonds : bond 0.03928 ( 748) hydrogen bonds : angle 4.45495 ( 2184) Misc. bond : bond 0.00119 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8865 (ptp) cc_final: 0.8659 (ptp) REVERT: A 118 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8027 (mt) REVERT: A 339 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7708 (mmmm) REVERT: A 352 LYS cc_start: 0.6039 (mmpt) cc_final: 0.4877 (pttt) REVERT: A 359 ASP cc_start: 0.7737 (m-30) cc_final: 0.7452 (m-30) REVERT: A 432 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6717 (mt-10) REVERT: A 501 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.6477 (mp10) REVERT: B 47 MET cc_start: 0.8857 (ptp) cc_final: 0.8656 (ptp) REVERT: B 118 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8078 (mt) REVERT: B 335 GLN cc_start: 0.7423 (tp40) cc_final: 0.7171 (pp30) REVERT: B 336 GLU cc_start: 0.7280 (tp30) cc_final: 0.6924 (tp30) REVERT: B 352 LYS cc_start: 0.6115 (mmpt) cc_final: 0.4930 (pttt) REVERT: B 359 ASP cc_start: 0.7778 (m-30) cc_final: 0.7513 (m-30) REVERT: B 432 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6750 (mt-10) REVERT: B 438 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6376 (pt0) REVERT: B 501 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.6511 (mp10) REVERT: C 210 ILE cc_start: 0.8177 (pt) cc_final: 0.7872 (tp) REVERT: C 336 GLU cc_start: 0.7341 (tp30) cc_final: 0.7056 (tp30) REVERT: C 352 LYS cc_start: 0.6100 (mmpt) cc_final: 0.4915 (pttt) REVERT: C 359 ASP cc_start: 0.7772 (m-30) cc_final: 0.7497 (m-30) REVERT: C 501 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.6557 (mp10) REVERT: D 47 MET cc_start: 0.8874 (ptp) cc_final: 0.8634 (ptp) REVERT: D 335 GLN cc_start: 0.7326 (tp40) cc_final: 0.7068 (pp30) REVERT: D 336 GLU cc_start: 0.7205 (tp30) cc_final: 0.6910 (tp30) REVERT: D 352 LYS cc_start: 0.5942 (mmpt) cc_final: 0.4695 (pttt) REVERT: D 359 ASP cc_start: 0.7778 (m-30) cc_final: 0.7468 (m-30) REVERT: D 432 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6706 (mt-10) REVERT: D 438 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6370 (pt0) REVERT: D 501 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.6440 (mp10) outliers start: 44 outliers final: 22 residues processed: 217 average time/residue: 0.6641 time to fit residues: 159.6250 Evaluate side-chains 206 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.134188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103698 restraints weight = 21038.926| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.88 r_work: 0.3105 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18304 Z= 0.174 Angle : 0.573 7.049 24844 Z= 0.288 Chirality : 0.046 0.275 2732 Planarity : 0.004 0.040 3164 Dihedral : 8.446 58.396 2908 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.14 % Allowed : 14.45 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2196 helix: 1.20 (0.16), residues: 1072 sheet: -0.10 (0.29), residues: 256 loop : 0.03 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.011 0.001 TYR A 97 PHE 0.029 0.002 PHE D 471 TRP 0.010 0.001 TRP B 558 HIS 0.006 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00426 (18288) covalent geometry : angle 0.57326 (24844) hydrogen bonds : bond 0.04174 ( 748) hydrogen bonds : angle 4.51709 ( 2184) Misc. bond : bond 0.00120 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8000 (mt) REVERT: A 179 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7891 (mm) REVERT: A 339 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7788 (mmmm) REVERT: A 352 LYS cc_start: 0.6045 (mmpt) cc_final: 0.4875 (pttt) REVERT: A 359 ASP cc_start: 0.7755 (m-30) cc_final: 0.7466 (m-30) REVERT: A 501 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.6543 (mp10) REVERT: B 118 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8050 (mt) REVERT: B 335 GLN cc_start: 0.7510 (tp40) cc_final: 0.6895 (mp-120) REVERT: B 336 GLU cc_start: 0.7286 (tp30) cc_final: 0.6851 (tp30) REVERT: B 352 LYS cc_start: 0.6035 (mmpt) cc_final: 0.4871 (pttt) REVERT: B 359 ASP cc_start: 0.7800 (m-30) cc_final: 0.7531 (m-30) REVERT: B 501 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: C 210 ILE cc_start: 0.8179 (pt) cc_final: 0.7857 (tp) REVERT: C 336 GLU cc_start: 0.7370 (tp30) cc_final: 0.7070 (tp30) REVERT: C 352 LYS cc_start: 0.6014 (mmpt) cc_final: 0.4852 (pttt) REVERT: C 359 ASP cc_start: 0.7792 (m-30) cc_final: 0.7514 (m-30) REVERT: C 501 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.6597 (mp10) REVERT: D 335 GLN cc_start: 0.7466 (tp40) cc_final: 0.7185 (pp30) REVERT: D 336 GLU cc_start: 0.7189 (tp30) cc_final: 0.6955 (tp30) REVERT: D 352 LYS cc_start: 0.5967 (mmpt) cc_final: 0.4712 (pttt) REVERT: D 359 ASP cc_start: 0.7787 (m-30) cc_final: 0.7473 (m-30) REVERT: D 432 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6691 (mt-10) REVERT: D 501 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.6500 (mp10) outliers start: 40 outliers final: 21 residues processed: 212 average time/residue: 0.6466 time to fit residues: 152.7038 Evaluate side-chains 203 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 91 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 214 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.136890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106492 restraints weight = 20817.132| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.89 r_work: 0.3155 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18304 Z= 0.114 Angle : 0.536 8.413 24844 Z= 0.268 Chirality : 0.043 0.266 2732 Planarity : 0.004 0.040 3164 Dihedral : 8.028 57.811 2908 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.71 % Allowed : 14.88 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2196 helix: 1.37 (0.16), residues: 1076 sheet: -0.06 (0.29), residues: 256 loop : 0.06 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 197 TYR 0.009 0.001 TYR C 112 PHE 0.025 0.001 PHE B 471 TRP 0.009 0.001 TRP B 558 HIS 0.005 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00266 (18288) covalent geometry : angle 0.53558 (24844) hydrogen bonds : bond 0.03540 ( 748) hydrogen bonds : angle 4.35559 ( 2184) Misc. bond : bond 0.00115 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7989 (mt) REVERT: A 352 LYS cc_start: 0.6042 (mmpt) cc_final: 0.4878 (pttt) REVERT: A 359 ASP cc_start: 0.7697 (m-30) cc_final: 0.7417 (m-30) REVERT: A 432 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6710 (mt-10) REVERT: A 501 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.6441 (mp10) REVERT: B 118 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8030 (mt) REVERT: B 335 GLN cc_start: 0.7385 (tp40) cc_final: 0.6793 (mp-120) REVERT: B 336 GLU cc_start: 0.7269 (tp30) cc_final: 0.6839 (tp30) REVERT: B 352 LYS cc_start: 0.6177 (mmpt) cc_final: 0.5006 (pttt) REVERT: B 359 ASP cc_start: 0.7784 (m-30) cc_final: 0.7521 (m-30) REVERT: B 501 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.6449 (mp10) REVERT: C 80 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7873 (mt-10) REVERT: C 210 ILE cc_start: 0.8173 (pt) cc_final: 0.7877 (tp) REVERT: C 336 GLU cc_start: 0.7324 (tp30) cc_final: 0.7033 (tp30) REVERT: C 352 LYS cc_start: 0.6060 (mmpt) cc_final: 0.4906 (pttt) REVERT: C 359 ASP cc_start: 0.7797 (m-30) cc_final: 0.7532 (m-30) REVERT: C 501 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.6526 (mp10) REVERT: D 335 GLN cc_start: 0.7375 (tp40) cc_final: 0.7032 (pp30) REVERT: D 336 GLU cc_start: 0.7191 (tp30) cc_final: 0.6841 (tp30) REVERT: D 339 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7792 (mmmm) REVERT: D 352 LYS cc_start: 0.6010 (mmpt) cc_final: 0.4725 (pttt) REVERT: D 359 ASP cc_start: 0.7783 (m-30) cc_final: 0.7480 (m-30) REVERT: D 432 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6732 (mt-10) REVERT: D 501 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.6418 (mp10) outliers start: 32 outliers final: 20 residues processed: 215 average time/residue: 0.6341 time to fit residues: 151.3471 Evaluate side-chains 200 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 501 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 1 optimal weight: 0.9990 chunk 175 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 159 optimal weight: 0.4980 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.137005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106520 restraints weight = 21033.149| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.90 r_work: 0.3148 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18304 Z= 0.118 Angle : 0.540 8.590 24844 Z= 0.269 Chirality : 0.044 0.282 2732 Planarity : 0.004 0.041 3164 Dihedral : 8.877 54.732 2908 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.71 % Allowed : 15.15 % Favored : 83.14 % 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: 0.99 (0.18), residues: 2196 helix: 1.42 (0.16), residues: 1076 sheet: -0.08 (0.29), residues: 256 loop : 0.05 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 197 TYR 0.008 0.001 TYR C 112 PHE 0.025 0.001 PHE B 471 TRP 0.008 0.001 TRP B 558 HIS 0.005 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00276 (18288) covalent geometry : angle 0.54033 (24844) hydrogen bonds : bond 0.03553 ( 748) hydrogen bonds : angle 4.31605 ( 2184) Misc. bond : bond 0.00134 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5663.11 seconds wall clock time: 97 minutes 32.94 seconds (5852.94 seconds total)