Starting phenix.real_space_refine on Sat Aug 8 21:26:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vku_65143/08_2026/9vku_65143_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vku_65143/08_2026/9vku_65143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vku_65143/08_2026/9vku_65143_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vku_65143/08_2026/9vku_65143_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vku_65143/08_2026/9vku_65143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vku_65143/08_2026/9vku_65143.map" } resolution = 3.49 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= 0.021 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: 6 Type Number sf(0) Gaussians P 652 5.49 5 Mg 7 5.21 5 S 36 5.16 5 C 16657 2.51 5 N 5178 2.21 5 O 7590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30120 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4117 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 18, 'TRANS': 480} Chain: "B" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4068 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 18, 'TRANS': 475} Chain: "C" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 4054 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 18, 'TRANS': 473} Chain: "D" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 4054 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 18, 'TRANS': 473} Chain: "E" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 3455 Classifications: {'RNA': 163} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 16, 'rna3p_pur': 67, 'rna3p_pyr': 71} Link IDs: {'rna2p': 24, 'rna3p': 138} Chain breaks: 2 Chain: "F" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 3455 Classifications: {'RNA': 163} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 17, 'rna3p_pur': 69, 'rna3p_pyr': 70} Link IDs: {'rna2p': 23, 'rna3p': 139} Chain breaks: 2 Chain: "G" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 3455 Classifications: {'RNA': 163} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 17, 'rna3p_pur': 70, 'rna3p_pyr': 70} Link IDs: {'rna2p': 22, 'rna3p': 140} Chain breaks: 2 Chain: "H" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 3455 Classifications: {'RNA': 163} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 17, 'rna3p_pur': 69, 'rna3p_pyr': 70} Link IDs: {'rna2p': 23, 'rna3p': 139} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.68, per 1000 atoms: 0.19 Number of scatterers: 30120 At special positions: 0 Unit cell: (125.4, 147.25, 193.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 652 15.00 Mg 7 11.99 O 7590 8.00 N 5178 7.00 C 16657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 575.3 milliseconds 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3778 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 15 sheets defined 62.4% alpha, 7.9% beta 184 base pairs and 339 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 2 through 38 Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.889A pdb=" N ASN A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 132 removed outlier: 3.643A pdb=" N PHE A 132 " --> pdb=" O ARG A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 132' Processing helix chain 'A' and resid 145 through 159 removed outlier: 3.689A pdb=" N ASP A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 184 removed outlier: 3.720A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 208 removed outlier: 3.573A pdb=" N ARG A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 226 removed outlier: 4.210A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.755A pdb=" N ASP A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'A' and resid 316 through 336 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.811A pdb=" N LYS A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 370 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 403 through 433 removed outlier: 4.088A pdb=" N LEU A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 468 through 490 removed outlier: 3.874A pdb=" N ILE A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N GLU A 486 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 41 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 69 through 84 Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.518A pdb=" N SER B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.566A pdb=" N ASN B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 159 Processing helix chain 'B' and resid 169 through 175 removed outlier: 3.603A pdb=" N SER B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 193 through 208 Processing helix chain 'B' and resid 215 through 226 removed outlier: 3.945A pdb=" N LEU B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 253 through 272 Processing helix chain 'B' and resid 316 through 336 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 355 through 370 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.639A pdb=" N PHE B 397 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 398 " --> pdb=" O MET B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 432 removed outlier: 3.904A pdb=" N LEU B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.989A pdb=" N LEU B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 468 through 490 removed outlier: 3.857A pdb=" N ILE B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ILE B 485 " --> pdb=" O GLN B 481 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N GLU B 486 " --> pdb=" O GLU B 482 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 40 Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.663A pdb=" N SER C 56 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 110 through 128 removed outlier: 3.771A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 132 removed outlier: 3.511A pdb=" N PHE C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 129 through 132' Processing helix chain 'C' and resid 145 through 159 Processing helix chain 'C' and resid 169 through 176 Processing helix chain 'C' and resid 177 through 184 removed outlier: 3.613A pdb=" N LEU C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 208 Processing helix chain 'C' and resid 215 through 226 removed outlier: 4.309A pdb=" N LEU C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 237 removed outlier: 3.735A pdb=" N ASP C 230 " --> pdb=" O CYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 272 removed outlier: 3.514A pdb=" N ASN C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN C 262 " --> pdb=" O CYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 336 Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 355 through 370 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 403 through 433 removed outlier: 4.066A pdb=" N LEU C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.622A pdb=" N ILE C 443 " --> pdb=" O PHE C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 Processing helix chain 'C' and resid 468 through 490 removed outlier: 3.874A pdb=" N ILE C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ILE C 485 " --> pdb=" O GLN C 481 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N GLU C 486 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 41 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 69 through 84 Processing helix chain 'D' and resid 110 through 128 removed outlier: 3.546A pdb=" N ASN D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 145 through 159 Processing helix chain 'D' and resid 169 through 175 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.601A pdb=" N LEU D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'D' and resid 193 through 207 removed outlier: 4.051A pdb=" N ARG D 207 " --> pdb=" O PHE D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 226 removed outlier: 3.726A pdb=" N LEU D 219 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 Processing helix chain 'D' and resid 253 through 272 Processing helix chain 'D' and resid 316 through 336 Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 355 through 370 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 393 through 397 removed outlier: 3.619A pdb=" N PHE D 397 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 432 removed outlier: 3.977A pdb=" N LEU D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 removed outlier: 3.956A pdb=" N LEU D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 456 Processing helix chain 'D' and resid 468 through 490 removed outlier: 3.777A pdb=" N ILE D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D 482 " --> pdb=" O LYS D 478 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ILE D 485 " --> pdb=" O GLN D 481 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N GLU D 486 " --> pdb=" O GLU D 482 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS D 487 " --> pdb=" O SER D 483 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 97 Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.555A pdb=" N THR A 247 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 303 Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 97 Processing sheet with id=AA5, first strand: chain 'B' and resid 239 through 242 removed outlier: 3.900A pdb=" N ASN B 276 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 239 through 242 removed outlier: 3.822A pdb=" N THR B 162 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 97 Processing sheet with id=AA9, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.924A pdb=" N ASN C 276 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB2, first strand: chain 'C' and resid 300 through 303 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 97 Processing sheet with id=AB4, first strand: chain 'D' and resid 239 through 241 removed outlier: 4.163A pdb=" N ASN D 276 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 239 through 241 Processing sheet with id=AB6, first strand: chain 'D' and resid 301 through 303 943 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 428 hydrogen bonds 574 hydrogen bond angles 0 basepair planarities 184 basepair parallelities 339 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5562 1.33 - 1.45: 10922 1.45 - 1.57: 14239 1.57 - 1.69: 1292 1.69 - 1.81: 52 Bond restraints: 32067 Sorted by residual: bond pdb=" C ARG A 242 " pdb=" N TYR A 243 " ideal model delta sigma weight residual 1.327 1.395 -0.068 1.06e-02 8.90e+03 4.08e+01 bond pdb=" C ASP C 445 " pdb=" N ARG C 446 " ideal model delta sigma weight residual 1.332 1.259 0.074 1.40e-02 5.10e+03 2.76e+01 bond pdb=" C ARG C 446 " pdb=" N GLU C 447 " ideal model delta sigma weight residual 1.335 1.279 0.056 1.31e-02 5.83e+03 1.80e+01 bond pdb=" C TYR D 243 " pdb=" N ALA D 244 " ideal model delta sigma weight residual 1.331 1.384 -0.054 1.37e-02 5.33e+03 1.53e+01 bond pdb=" C TYR A 243 " pdb=" N ALA A 244 " ideal model delta sigma weight residual 1.330 1.378 -0.048 1.41e-02 5.03e+03 1.14e+01 ... (remaining 32062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 43574 1.65 - 3.31: 2482 3.31 - 4.96: 232 4.96 - 6.61: 65 6.61 - 8.27: 7 Bond angle restraints: 46360 Sorted by residual: angle pdb=" O5' C H 35 " pdb=" C5' C H 35 " pdb=" C4' C H 35 " ideal model delta sigma weight residual 109.40 113.52 -4.12 8.00e-01 1.56e+00 2.65e+01 angle pdb=" O5' A G 111 " pdb=" C5' A G 111 " pdb=" C4' A G 111 " ideal model delta sigma weight residual 109.40 113.31 -3.91 8.00e-01 1.56e+00 2.39e+01 angle pdb=" O5' C E 35 " pdb=" C5' C E 35 " pdb=" C4' C E 35 " ideal model delta sigma weight residual 109.40 113.28 -3.88 8.00e-01 1.56e+00 2.35e+01 angle pdb=" CA ASP C 445 " pdb=" C ASP C 445 " pdb=" N ARG C 446 " ideal model delta sigma weight residual 116.87 124.42 -7.55 1.56e+00 4.11e-01 2.35e+01 angle pdb=" C1' G H 143 " pdb=" N9 G H 143 " pdb=" C4 G H 143 " ideal model delta sigma weight residual 126.50 132.63 -6.13 1.30e+00 5.92e-01 2.22e+01 ... (remaining 46355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 18534 35.80 - 71.59: 1663 71.59 - 107.39: 173 107.39 - 143.19: 12 143.19 - 178.98: 12 Dihedral angle restraints: 20394 sinusoidal: 14553 harmonic: 5841 Sorted by residual: dihedral pdb=" CD ARG D 242 " pdb=" NE ARG D 242 " pdb=" CZ ARG D 242 " pdb=" NH1 ARG D 242 " ideal model delta sinusoidal sigma weight residual 0.00 87.36 -87.36 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" O4' U H 124 " pdb=" C1' U H 124 " pdb=" N1 U H 124 " pdb=" C2 U H 124 " ideal model delta sinusoidal sigma weight residual 232.00 53.02 178.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U G 127 " pdb=" C1' U G 127 " pdb=" N1 U G 127 " pdb=" C2 U G 127 " ideal model delta sinusoidal sigma weight residual 232.00 53.26 178.74 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 20391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5191 0.103 - 0.206: 416 0.206 - 0.309: 4 0.309 - 0.412: 0 0.412 - 0.515: 36 Chirality restraints: 5647 Sorted by residual: chirality pdb=" P U F 63 " pdb=" OP1 U F 63 " pdb=" OP2 U F 63 " pdb=" O5' U F 63 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" P A G 65 " pdb=" OP1 A G 65 " pdb=" OP2 A G 65 " pdb=" O5' A G 65 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" P C H 68 " pdb=" OP1 C H 68 " pdb=" OP2 C H 68 " pdb=" O5' C H 68 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.44e+00 ... (remaining 5644 not shown) Planarity restraints: 3502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 242 " -1.107 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG D 242 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG D 242 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 242 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 242 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.663 9.50e-02 1.11e+02 2.97e-01 5.39e+01 pdb=" NE ARG A 28 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 388 " 0.421 9.50e-02 1.11e+02 1.89e-01 2.21e+01 pdb=" NE ARG B 388 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 388 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 388 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 388 " 0.012 2.00e-02 2.50e+03 ... (remaining 3499 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 96 2.46 - 3.07: 19711 3.07 - 3.68: 54834 3.68 - 4.29: 76931 4.29 - 4.90: 111379 Nonbonded interactions: 262951 Sorted by model distance: nonbonded pdb=" O2' A H 96 " pdb=" OP1 A H 97 " model vdw 1.845 3.040 nonbonded pdb=" O2' G H 38 " pdb=" OP1 U H 39 " model vdw 1.921 3.040 nonbonded pdb=" OP2 C F 109 " pdb=" O2' A F 110 " model vdw 1.930 3.040 nonbonded pdb=" O2' G G 38 " pdb=" OP1 U G 39 " model vdw 1.962 3.040 nonbonded pdb=" O2' G E 38 " pdb=" OP1 U E 39 " model vdw 1.974 3.040 ... (remaining 262946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 492) selection = (chain 'B' and resid 1 through 492) selection = chain 'C' selection = (chain 'D' and resid 1 through 492) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.700 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: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.670 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32067 Z= 0.265 Angle : 0.765 8.268 46360 Z= 0.603 Chirality : 0.061 0.515 5647 Planarity : 0.012 0.496 3502 Dihedral : 22.013 178.983 16616 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.39 % Allowed : 8.09 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.20), residues: 1969 helix: 1.33 (0.16), residues: 1077 sheet: -1.44 (0.44), residues: 140 loop : -1.07 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 388 TYR 0.018 0.001 TYR D 243 PHE 0.035 0.001 PHE B 240 TRP 0.012 0.001 TRP A 227 HIS 0.008 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.27 (32067) covalent geometry : angle 0.76530 / 0.60 (46360) hydrogen bonds : bond 0.14397 / 9.40 ( 1346) hydrogen bonds : angle 5.66644 / 4.02 ( 3226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 295 time to evaluate : 0.845 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8918 (mt0) cc_final: 0.8565 (mt0) REVERT: A 54 TYR cc_start: 0.9025 (p90) cc_final: 0.8778 (p90) REVERT: A 183 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8792 (mm-30) REVERT: A 230 ASP cc_start: 0.8228 (m-30) cc_final: 0.7935 (m-30) REVERT: A 453 CYS cc_start: 0.8730 (m) cc_final: 0.8470 (m) REVERT: B 369 MET cc_start: 0.7798 (mtm) cc_final: 0.7590 (mtp) REVERT: B 380 ASP cc_start: 0.9494 (m-30) cc_final: 0.8894 (t70) REVERT: C 118 LYS cc_start: 0.9437 (ttmt) cc_final: 0.9197 (ttmm) REVERT: C 378 ILE cc_start: 0.9689 (mt) cc_final: 0.9478 (mm) REVERT: D 14 GLU cc_start: 0.9108 (tp30) cc_final: 0.8288 (tt0) REVERT: D 46 ASP cc_start: 0.8606 (m-30) cc_final: 0.8399 (p0) REVERT: D 118 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9128 (tmtt) REVERT: D 231 GLN cc_start: 0.8490 (tt0) cc_final: 0.8178 (tm-30) REVERT: D 381 TYR cc_start: 0.9210 (t80) cc_final: 0.8842 (t80) outliers start: 7 outliers final: 3 residues processed: 300 average time/residue: 0.2073 time to fit residues: 97.7798 Evaluate side-chains 138 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 29 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.0370 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 50.0000 overall best weight: 5.8068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.055544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.040586 restraints weight = 196205.107| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.38 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 32067 Z= 0.235 Angle : 0.668 10.873 46360 Z= 0.364 Chirality : 0.043 0.468 5647 Planarity : 0.007 0.239 3502 Dihedral : 23.278 178.489 12400 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.27 % Allowed : 11.80 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1969 helix: 1.69 (0.15), residues: 1094 sheet: -1.08 (0.45), residues: 144 loop : -0.94 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 242 TYR 0.046 0.002 TYR D 243 PHE 0.016 0.002 PHE D 169 TRP 0.016 0.002 TRP A 227 HIS 0.008 0.002 HIS C 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.24 (32067) covalent geometry : angle 0.66795 / 0.36 (46360) hydrogen bonds : bond 0.08702 / 5.52 ( 1346) hydrogen bonds : angle 4.22484 / 3.02 ( 3226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8904 (mt0) cc_final: 0.8619 (mt0) REVERT: A 54 TYR cc_start: 0.9127 (p90) cc_final: 0.8908 (p90) REVERT: A 196 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8726 (mt-10) REVERT: A 281 GLU cc_start: 0.8368 (mp0) cc_final: 0.7933 (mp0) REVERT: A 453 CYS cc_start: 0.9138 (m) cc_final: 0.8743 (m) REVERT: A 458 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8608 (mm) REVERT: B 380 ASP cc_start: 0.9510 (m-30) cc_final: 0.9174 (m-30) REVERT: B 489 MET cc_start: 0.9300 (tpp) cc_final: 0.8834 (mmt) REVERT: C 185 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8865 (m-80) REVERT: D 46 ASP cc_start: 0.8813 (m-30) cc_final: 0.8520 (p0) REVERT: D 118 LYS cc_start: 0.9451 (mtpp) cc_final: 0.9161 (tmtt) REVERT: D 231 GLN cc_start: 0.8577 (tt0) cc_final: 0.8126 (tm-30) REVERT: D 243 TYR cc_start: 0.8085 (p90) cc_final: 0.7815 (p90) REVERT: D 369 MET cc_start: 0.7750 (mtm) cc_final: 0.7022 (mtm) REVERT: D 381 TYR cc_start: 0.9556 (t80) cc_final: 0.9117 (t80) REVERT: D 469 PHE cc_start: 0.9072 (m-80) cc_final: 0.8786 (m-10) outliers start: 41 outliers final: 18 residues processed: 166 average time/residue: 0.1694 time to fit residues: 47.2897 Evaluate side-chains 119 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 226 CYS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 450 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 164 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 237 optimal weight: 50.0000 chunk 173 optimal weight: 0.9980 chunk 238 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 242 optimal weight: 50.0000 chunk 203 optimal weight: 50.0000 chunk 142 optimal weight: 9.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 357 ASN B 387 ASN ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 223 ASN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.055324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.040487 restraints weight = 196124.909| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.35 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32067 Z= 0.165 Angle : 0.558 10.959 46360 Z= 0.311 Chirality : 0.038 0.476 5647 Planarity : 0.004 0.106 3502 Dihedral : 23.268 178.626 12397 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.99 % Allowed : 12.47 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1969 helix: 1.95 (0.16), residues: 1108 sheet: -0.72 (0.47), residues: 142 loop : -0.90 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 35 TYR 0.030 0.002 TYR D 243 PHE 0.017 0.002 PHE D 173 TRP 0.015 0.002 TRP C 432 HIS 0.008 0.002 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (32067) covalent geometry : angle 0.55800 / 0.31 (46360) hydrogen bonds : bond 0.07786 / 4.97 ( 1346) hydrogen bonds : angle 3.91964 / 2.81 ( 3226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8836 (mt0) cc_final: 0.8533 (mt0) REVERT: A 14 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: A 54 TYR cc_start: 0.9090 (p90) cc_final: 0.8878 (p90) REVERT: A 164 LEU cc_start: 0.9700 (OUTLIER) cc_final: 0.9481 (mp) REVERT: A 283 ILE cc_start: 0.9530 (mt) cc_final: 0.9126 (mm) REVERT: A 294 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: A 453 CYS cc_start: 0.9175 (m) cc_final: 0.8803 (m) REVERT: B 380 ASP cc_start: 0.9462 (m-30) cc_final: 0.9106 (m-30) REVERT: C 171 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8268 (p0) REVERT: C 185 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8846 (m-80) REVERT: D 46 ASP cc_start: 0.8825 (m-30) cc_final: 0.8624 (p0) REVERT: D 118 LYS cc_start: 0.9439 (mtpp) cc_final: 0.9111 (tmtt) REVERT: D 231 GLN cc_start: 0.8720 (tt0) cc_final: 0.8248 (tm-30) REVERT: D 369 MET cc_start: 0.7706 (mtm) cc_final: 0.7073 (mtm) REVERT: D 381 TYR cc_start: 0.9522 (t80) cc_final: 0.9140 (t80) REVERT: D 395 MET cc_start: 0.8956 (tpp) cc_final: 0.8689 (tpp) REVERT: D 469 PHE cc_start: 0.9014 (m-80) cc_final: 0.8519 (m-10) outliers start: 36 outliers final: 16 residues processed: 131 average time/residue: 0.1542 time to fit residues: 35.4858 Evaluate side-chains 106 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 450 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 147 optimal weight: 8.9990 chunk 256 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 222 optimal weight: 40.0000 chunk 236 optimal weight: 50.0000 chunk 105 optimal weight: 10.0000 chunk 211 optimal weight: 50.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS D 89 ASN D 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.053167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.038508 restraints weight = 197497.462| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.46 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 32067 Z= 0.248 Angle : 0.612 9.006 46360 Z= 0.337 Chirality : 0.041 0.454 5647 Planarity : 0.005 0.109 3502 Dihedral : 23.314 179.393 12397 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 2.94 % Allowed : 12.02 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.20), residues: 1969 helix: 1.89 (0.15), residues: 1108 sheet: -0.70 (0.47), residues: 142 loop : -0.92 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 242 TYR 0.021 0.002 TYR A 329 PHE 0.016 0.002 PHE D 203 TRP 0.014 0.002 TRP A 227 HIS 0.008 0.002 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.25 (32067) covalent geometry : angle 0.61246 / 0.34 (46360) hydrogen bonds : bond 0.08645 / 5.55 ( 1346) hydrogen bonds : angle 4.02889 / 2.90 ( 3226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 89 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8953 (mt0) cc_final: 0.8711 (mt0) REVERT: A 14 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8525 (mt-10) REVERT: A 54 TYR cc_start: 0.9138 (p90) cc_final: 0.8909 (p90) REVERT: A 164 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9516 (mp) REVERT: A 166 GLU cc_start: 0.8532 (mp0) cc_final: 0.8320 (mp0) REVERT: A 283 ILE cc_start: 0.9519 (mt) cc_final: 0.9244 (mm) REVERT: A 294 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: A 395 MET cc_start: 0.9045 (mmm) cc_final: 0.8670 (mmm) REVERT: A 453 CYS cc_start: 0.9198 (m) cc_final: 0.8775 (m) REVERT: B 295 ILE cc_start: 0.8309 (mt) cc_final: 0.7942 (mp) REVERT: B 363 CYS cc_start: 0.8937 (m) cc_final: 0.8691 (m) REVERT: B 380 ASP cc_start: 0.9446 (m-30) cc_final: 0.9112 (m-30) REVERT: B 444 LEU cc_start: 0.8479 (mm) cc_final: 0.8028 (mm) REVERT: C 94 LYS cc_start: 0.9052 (tptp) cc_final: 0.8821 (tptp) REVERT: C 151 ASP cc_start: 0.9230 (OUTLIER) cc_final: 0.8961 (m-30) REVERT: C 171 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8408 (p0) REVERT: D 118 LYS cc_start: 0.9480 (mtpp) cc_final: 0.9177 (tmtt) REVERT: D 223 ASN cc_start: 0.9349 (OUTLIER) cc_final: 0.9139 (t0) REVERT: D 231 GLN cc_start: 0.8779 (tt0) cc_final: 0.8330 (tm-30) REVERT: D 369 MET cc_start: 0.7839 (mtm) cc_final: 0.7231 (mtm) REVERT: D 381 TYR cc_start: 0.9600 (t80) cc_final: 0.9299 (t80) REVERT: D 469 PHE cc_start: 0.9168 (m-80) cc_final: 0.8806 (m-10) outliers start: 53 outliers final: 29 residues processed: 135 average time/residue: 0.1502 time to fit residues: 35.5115 Evaluate side-chains 111 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 226 CYS Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 450 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 114 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 148 optimal weight: 5.9990 chunk 208 optimal weight: 50.0000 chunk 105 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 200 optimal weight: 50.0000 chunk 227 optimal weight: 50.0000 chunk 206 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 HIS ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN C 26 HIS D 89 ASN D 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.054413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.039553 restraints weight = 197117.287| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.40 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 32067 Z= 0.119 Angle : 0.508 10.150 46360 Z= 0.286 Chirality : 0.036 0.459 5647 Planarity : 0.004 0.046 3502 Dihedral : 23.283 179.454 12397 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.72 % Allowed : 13.85 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1969 helix: 2.19 (0.16), residues: 1111 sheet: -0.74 (0.47), residues: 144 loop : -0.81 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 131 TYR 0.022 0.001 TYR A 329 PHE 0.015 0.001 PHE C 121 TRP 0.010 0.001 TRP C 250 HIS 0.008 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (32067) covalent geometry : angle 0.50832 / 0.29 (46360) hydrogen bonds : bond 0.07318 / 4.67 ( 1346) hydrogen bonds : angle 3.72363 / 2.68 ( 3226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8894 (mt0) cc_final: 0.8687 (mt0) REVERT: A 14 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8401 (mt-10) REVERT: A 54 TYR cc_start: 0.9128 (p90) cc_final: 0.8914 (p90) REVERT: A 164 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9516 (mp) REVERT: A 283 ILE cc_start: 0.9533 (mt) cc_final: 0.9312 (mm) REVERT: A 294 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: A 395 MET cc_start: 0.8876 (mmm) cc_final: 0.8631 (mmm) REVERT: A 453 CYS cc_start: 0.9119 (m) cc_final: 0.8773 (m) REVERT: B 253 GLU cc_start: 0.7881 (pm20) cc_final: 0.7625 (pm20) REVERT: B 363 CYS cc_start: 0.8932 (m) cc_final: 0.8689 (m) REVERT: B 380 ASP cc_start: 0.9413 (m-30) cc_final: 0.9064 (m-30) REVERT: B 444 LEU cc_start: 0.8437 (mm) cc_final: 0.7992 (mm) REVERT: B 489 MET cc_start: 0.9253 (tpp) cc_final: 0.9051 (mmt) REVERT: C 151 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8908 (m-30) REVERT: C 171 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8288 (p0) REVERT: D 1 MET cc_start: 0.8357 (mtt) cc_final: 0.8071 (ttm) REVERT: D 118 LYS cc_start: 0.9432 (mtpp) cc_final: 0.9120 (tmtt) REVERT: D 369 MET cc_start: 0.7704 (mtm) cc_final: 0.7107 (mtm) REVERT: D 381 TYR cc_start: 0.9554 (t80) cc_final: 0.9275 (t80) REVERT: D 469 PHE cc_start: 0.9094 (m-80) cc_final: 0.8682 (m-10) REVERT: D 486 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8560 (tm-30) outliers start: 31 outliers final: 21 residues processed: 122 average time/residue: 0.1581 time to fit residues: 33.8269 Evaluate side-chains 108 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 450 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 77 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 109 optimal weight: 0.0570 chunk 246 optimal weight: 50.0000 chunk 222 optimal weight: 40.0000 chunk 239 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.054035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039254 restraints weight = 197421.500| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.40 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 32067 Z= 0.146 Angle : 0.510 9.652 46360 Z= 0.286 Chirality : 0.037 0.455 5647 Planarity : 0.004 0.042 3502 Dihedral : 23.220 179.172 12397 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.05 % Allowed : 14.46 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1969 helix: 2.23 (0.16), residues: 1111 sheet: -0.76 (0.46), residues: 144 loop : -0.84 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 131 TYR 0.037 0.001 TYR D 243 PHE 0.016 0.001 PHE D 132 TRP 0.011 0.001 TRP C 250 HIS 0.008 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (32067) covalent geometry : angle 0.50992 / 0.29 (46360) hydrogen bonds : bond 0.07279 / 4.67 ( 1346) hydrogen bonds : angle 3.71362 / 2.68 ( 3226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8903 (mt0) cc_final: 0.8694 (mt0) REVERT: A 14 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: A 54 TYR cc_start: 0.9146 (p90) cc_final: 0.8930 (p90) REVERT: A 283 ILE cc_start: 0.9542 (mt) cc_final: 0.9312 (mm) REVERT: A 294 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: A 395 MET cc_start: 0.8974 (mmm) cc_final: 0.8619 (mmm) REVERT: A 453 CYS cc_start: 0.9145 (m) cc_final: 0.8811 (m) REVERT: B 334 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7406 (t0) REVERT: B 363 CYS cc_start: 0.8947 (m) cc_final: 0.8711 (m) REVERT: B 380 ASP cc_start: 0.9415 (m-30) cc_final: 0.9066 (m-30) REVERT: C 151 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8953 (m-30) REVERT: C 171 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8323 (p0) REVERT: D 1 MET cc_start: 0.8318 (mtt) cc_final: 0.8013 (ttm) REVERT: D 118 LYS cc_start: 0.9439 (mtpp) cc_final: 0.9131 (tmtt) REVERT: D 369 MET cc_start: 0.7725 (mtm) cc_final: 0.7137 (mtm) REVERT: D 381 TYR cc_start: 0.9551 (t80) cc_final: 0.9288 (t80) REVERT: D 469 PHE cc_start: 0.9119 (m-80) cc_final: 0.8695 (m-10) REVERT: D 486 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8616 (tm-30) outliers start: 37 outliers final: 25 residues processed: 116 average time/residue: 0.1564 time to fit residues: 31.6735 Evaluate side-chains 109 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 226 CYS Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 450 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 31 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 201 optimal weight: 50.0000 chunk 100 optimal weight: 2.9990 chunk 251 optimal weight: 40.0000 chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** 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 = 0.3520 r_free = 0.3520 target = 0.053858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.039128 restraints weight = 200007.125| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.42 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32067 Z= 0.143 Angle : 0.510 9.317 46360 Z= 0.284 Chirality : 0.037 0.457 5647 Planarity : 0.004 0.041 3502 Dihedral : 23.180 178.807 12397 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 2.55 % Allowed : 14.46 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1969 helix: 2.30 (0.15), residues: 1110 sheet: -0.74 (0.46), residues: 144 loop : -0.87 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 131 TYR 0.025 0.001 TYR D 86 PHE 0.017 0.001 PHE C 121 TRP 0.013 0.001 TRP A 250 HIS 0.008 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (32067) covalent geometry : angle 0.51029 / 0.28 (46360) hydrogen bonds : bond 0.07058 / 4.57 ( 1346) hydrogen bonds : angle 3.65503 / 2.64 ( 3226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 88 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8918 (mt0) cc_final: 0.8691 (mt0) REVERT: A 14 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8490 (mt-10) REVERT: A 54 TYR cc_start: 0.9155 (p90) cc_final: 0.8930 (p90) REVERT: A 166 GLU cc_start: 0.8448 (mp0) cc_final: 0.8238 (mp0) REVERT: A 283 ILE cc_start: 0.9531 (mt) cc_final: 0.9328 (mm) REVERT: A 389 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8649 (tt) REVERT: A 453 CYS cc_start: 0.9094 (m) cc_final: 0.8720 (m) REVERT: B 334 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7379 (t0) REVERT: B 363 CYS cc_start: 0.8943 (m) cc_final: 0.8706 (m) REVERT: B 380 ASP cc_start: 0.9379 (m-30) cc_final: 0.9171 (m-30) REVERT: B 411 ASP cc_start: 0.8485 (m-30) cc_final: 0.8196 (t0) REVERT: B 444 LEU cc_start: 0.8321 (mm) cc_final: 0.7842 (mm) REVERT: C 151 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8964 (m-30) REVERT: C 171 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8321 (p0) REVERT: C 215 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8734 (m) REVERT: C 302 ASP cc_start: 0.8754 (m-30) cc_final: 0.8271 (p0) REVERT: D 118 LYS cc_start: 0.9444 (mtpp) cc_final: 0.9146 (tmtt) REVERT: D 369 MET cc_start: 0.7724 (mtm) cc_final: 0.7142 (mtm) REVERT: D 381 TYR cc_start: 0.9544 (t80) cc_final: 0.9296 (t80) REVERT: D 469 PHE cc_start: 0.9124 (m-80) cc_final: 0.8690 (m-10) REVERT: D 486 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8575 (tm-30) outliers start: 46 outliers final: 30 residues processed: 127 average time/residue: 0.1728 time to fit residues: 38.1455 Evaluate side-chains 111 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 450 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 203 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 247 optimal weight: 50.0000 chunk 45 optimal weight: 7.9990 chunk 249 optimal weight: 50.0000 chunk 80 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 241 optimal weight: 50.0000 chunk 116 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 197 optimal weight: 50.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN C 492 GLN D 69 ASN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.053035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.038600 restraints weight = 198109.355| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.45 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32067 Z= 0.190 Angle : 0.542 8.604 46360 Z= 0.300 Chirality : 0.038 0.457 5647 Planarity : 0.004 0.040 3502 Dihedral : 23.200 179.519 12397 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.94 % Allowed : 15.24 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1969 helix: 2.28 (0.16), residues: 1108 sheet: -0.77 (0.46), residues: 144 loop : -0.93 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 131 TYR 0.023 0.002 TYR A 254 PHE 0.023 0.002 PHE A 121 TRP 0.010 0.001 TRP C 250 HIS 0.008 0.002 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (32067) covalent geometry : angle 0.54176 / 0.30 (46360) hydrogen bonds : bond 0.07454 / 4.85 ( 1346) hydrogen bonds : angle 3.75082 / 2.72 ( 3226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8924 (mt0) cc_final: 0.8690 (mt0) REVERT: A 14 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8511 (mt-10) REVERT: A 395 MET cc_start: 0.9019 (mmm) cc_final: 0.8763 (mmm) REVERT: A 453 CYS cc_start: 0.9122 (m) cc_final: 0.8726 (m) REVERT: B 363 CYS cc_start: 0.8917 (m) cc_final: 0.8699 (m) REVERT: B 411 ASP cc_start: 0.8457 (m-30) cc_final: 0.8200 (t0) REVERT: C 171 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8368 (p0) REVERT: C 217 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9287 (mp) REVERT: C 302 ASP cc_start: 0.8725 (m-30) cc_final: 0.8329 (p0) REVERT: D 1 MET cc_start: 0.8186 (mtm) cc_final: 0.7888 (ttm) REVERT: D 14 GLU cc_start: 0.8891 (tp30) cc_final: 0.8320 (tp30) REVERT: D 118 LYS cc_start: 0.9460 (mtpp) cc_final: 0.9121 (tmtt) REVERT: D 369 MET cc_start: 0.7759 (mtm) cc_final: 0.7244 (mtm) REVERT: D 381 TYR cc_start: 0.9534 (t80) cc_final: 0.9317 (t80) REVERT: D 468 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.8109 (p) REVERT: D 469 PHE cc_start: 0.9131 (m-80) cc_final: 0.8651 (m-10) REVERT: D 486 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8613 (tm-30) outliers start: 35 outliers final: 27 residues processed: 101 average time/residue: 0.1729 time to fit residues: 30.7705 Evaluate side-chains 98 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 468 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 181 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 242 optimal weight: 50.0000 chunk 27 optimal weight: 5.9990 chunk 239 optimal weight: 30.0000 chunk 129 optimal weight: 4.9990 chunk 227 optimal weight: 40.0000 chunk 89 optimal weight: 2.9990 chunk 235 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** 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 = 0.3509 r_free = 0.3509 target = 0.053128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038399 restraints weight = 201739.191| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.48 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32067 Z= 0.170 Angle : 0.524 8.981 46360 Z= 0.292 Chirality : 0.037 0.460 5647 Planarity : 0.004 0.040 3502 Dihedral : 23.225 179.938 12397 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.77 % Allowed : 15.62 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1969 helix: 2.29 (0.16), residues: 1109 sheet: -0.76 (0.46), residues: 144 loop : -0.94 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 131 TYR 0.025 0.001 TYR A 254 PHE 0.016 0.001 PHE A 121 TRP 0.011 0.001 TRP C 250 HIS 0.016 0.002 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (32067) covalent geometry : angle 0.52431 / 0.29 (46360) hydrogen bonds : bond 0.07333 / 4.78 ( 1346) hydrogen bonds : angle 3.68754 / 2.67 ( 3226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8906 (mt0) cc_final: 0.8660 (mt0) REVERT: A 14 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8523 (mt-10) REVERT: A 166 GLU cc_start: 0.8475 (mp0) cc_final: 0.8243 (mp0) REVERT: A 395 MET cc_start: 0.9044 (mmm) cc_final: 0.8782 (mmm) REVERT: A 453 CYS cc_start: 0.9121 (m) cc_final: 0.8735 (m) REVERT: B 334 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7350 (t0) REVERT: B 363 CYS cc_start: 0.8932 (m) cc_final: 0.8712 (m) REVERT: B 411 ASP cc_start: 0.8494 (m-30) cc_final: 0.8256 (t0) REVERT: B 444 LEU cc_start: 0.8384 (mm) cc_final: 0.8002 (mm) REVERT: C 171 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8380 (p0) REVERT: C 302 ASP cc_start: 0.8702 (m-30) cc_final: 0.8419 (p0) REVERT: D 14 GLU cc_start: 0.8887 (tp30) cc_final: 0.8345 (tp30) REVERT: D 118 LYS cc_start: 0.9460 (mtpp) cc_final: 0.9124 (tmtt) REVERT: D 369 MET cc_start: 0.7815 (mtm) cc_final: 0.7257 (mtm) REVERT: D 381 TYR cc_start: 0.9552 (t80) cc_final: 0.9318 (t80) REVERT: D 469 PHE cc_start: 0.9150 (m-80) cc_final: 0.8694 (m-10) REVERT: D 486 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8600 (tm-30) outliers start: 32 outliers final: 24 residues processed: 96 average time/residue: 0.1676 time to fit residues: 28.7072 Evaluate side-chains 93 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 226 CYS Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 450 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 223 optimal weight: 40.0000 chunk 99 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.053501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.039125 restraints weight = 194721.695| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.50 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32067 Z= 0.128 Angle : 0.500 9.944 46360 Z= 0.279 Chirality : 0.036 0.462 5647 Planarity : 0.003 0.041 3502 Dihedral : 23.182 179.427 12397 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.39 % Allowed : 16.18 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1969 helix: 2.40 (0.16), residues: 1109 sheet: -0.57 (0.47), residues: 144 loop : -0.83 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.022 0.001 TYR B 243 PHE 0.017 0.001 PHE A 121 TRP 0.012 0.001 TRP A 227 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (32067) covalent geometry : angle 0.49963 / 0.28 (46360) hydrogen bonds : bond 0.06962 / 4.57 ( 1346) hydrogen bonds : angle 3.57380 / 2.59 ( 3226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3938 Ramachandran restraints generated. 1969 Oldfield, 0 Emsley, 1969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8908 (mt0) cc_final: 0.8668 (mt0) REVERT: A 14 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: A 226 CYS cc_start: 0.8704 (t) cc_final: 0.8289 (t) REVERT: A 395 MET cc_start: 0.8977 (mmm) cc_final: 0.8725 (mmm) REVERT: A 453 CYS cc_start: 0.9079 (m) cc_final: 0.8729 (m) REVERT: B 334 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7202 (t0) REVERT: B 363 CYS cc_start: 0.8926 (m) cc_final: 0.8694 (m) REVERT: B 411 ASP cc_start: 0.8535 (m-30) cc_final: 0.8292 (t0) REVERT: C 171 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8359 (p0) REVERT: D 118 LYS cc_start: 0.9453 (mtpp) cc_final: 0.9144 (tmtt) REVERT: D 296 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8025 (t) REVERT: D 369 MET cc_start: 0.7716 (mtm) cc_final: 0.7158 (mtm) REVERT: D 381 TYR cc_start: 0.9528 (t80) cc_final: 0.9284 (t80) REVERT: D 469 PHE cc_start: 0.9156 (m-80) cc_final: 0.8657 (m-10) REVERT: D 486 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8571 (tm-30) outliers start: 25 outliers final: 20 residues processed: 96 average time/residue: 0.1707 time to fit residues: 29.0386 Evaluate side-chains 95 residues out of total 1805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 450 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 111 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 209 optimal weight: 40.0000 chunk 59 optimal weight: 8.9990 chunk 222 optimal weight: 40.0000 chunk 24 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 254 optimal weight: 40.0000 chunk 249 optimal weight: 50.0000 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.052607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037955 restraints weight = 203973.735| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.48 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32067 Z= 0.207 Angle : 0.551 9.107 46360 Z= 0.304 Chirality : 0.038 0.462 5647 Planarity : 0.004 0.040 3502 Dihedral : 23.225 178.609 12397 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.39 % Allowed : 16.34 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1969 helix: 2.28 (0.16), residues: 1109 sheet: -0.65 (0.47), residues: 144 loop : -0.94 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 366 TYR 0.026 0.002 TYR A 254 PHE 0.015 0.002 PHE B 442 TRP 0.009 0.001 TRP C 250 HIS 0.008 0.002 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (32067) covalent geometry : angle 0.55074 / 0.30 (46360) hydrogen bonds : bond 0.07751 / 5.08 ( 1346) hydrogen bonds : angle 3.76970 / 2.73 ( 3226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4619.52 seconds wall clock time: 81 minutes 11.61 seconds (4871.61 seconds total)