Starting phenix.real_space_refine on Thu Aug 6 04:13:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx0_37896/08_2026/8wx0_37896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx0_37896/08_2026/8wx0_37896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wx0_37896/08_2026/8wx0_37896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx0_37896/08_2026/8wx0_37896.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx0_37896/08_2026/8wx0_37896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx0_37896/08_2026/8wx0_37896.cif" } resolution = 3.7 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= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 49 5.16 5 C 8536 2.51 5 N 2338 2.21 5 O 2738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 13672 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4478 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 29, 'TRANS': 567} Chain: "B" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4447 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 29, 'TRANS': 562} Chain: "C" Number of atoms: 4452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4452 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 29, 'TRANS': 563} Chain: "E" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 3} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "G" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.76, per 1000 atoms: 0.28 Number of scatterers: 13672 At special positions: 0 Unit cell: (110.88, 103.84, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 11 15.00 O 2738 8.00 N 2338 7.00 C 8536 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: 1.06 Conformation dependent library (CDL) restraints added in 683.2 milliseconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 36.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 97 through 115 Proline residue: A 110 - end of helix Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.873A pdb=" N GLN A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 282 Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 294 through 314 removed outlier: 3.855A pdb=" N GLU A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 344 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.828A pdb=" N THR A 418 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.725A pdb=" N PHE A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 584 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 98 through 112 removed outlier: 3.974A pdb=" N CYS B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 138 through 154 removed outlier: 3.844A pdb=" N GLY B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.693A pdb=" N ARG B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 236 through 246 Processing helix chain 'B' and resid 253 through 258 removed outlier: 4.065A pdb=" N SER B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 removed outlier: 3.556A pdb=" N TYR B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.638A pdb=" N LEU B 286 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 287 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 314 removed outlier: 3.924A pdb=" N ILE B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 343 Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.507A pdb=" N THR B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 469 through 485 Processing helix chain 'B' and resid 558 through 584 removed outlier: 4.146A pdb=" N ALA B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.658A pdb=" N GLY C 23 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 97 through 112 Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 138 through 153 Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.675A pdb=" N GLU C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 273 through 282 removed outlier: 3.523A pdb=" N SER C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 297 through 314 removed outlier: 3.836A pdb=" N ARG C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU C 304 " --> pdb=" O GLN C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 342 Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.690A pdb=" N THR C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 469 through 485 Processing helix chain 'C' and resid 525 through 532 Processing helix chain 'C' and resid 558 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.095A pdb=" N PHE A 187 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP A 188 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA A 207 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 190 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 205 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 192 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N MET A 203 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR A 541 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 535 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 536 " --> pdb=" O MET A 497 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 521 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 362 removed outlier: 6.777A pdb=" N LEU A 382 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA A 462 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 384 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER A 460 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR A 386 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLN A 458 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ASP A 388 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE A 456 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 18 Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 175 removed outlier: 6.781A pdb=" N ASP B 188 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 207 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 190 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 205 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 192 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N MET B 203 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 551 " --> pdb=" O ASP B 535 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 535 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.200A pdb=" N GLN B 380 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET B 408 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N SER B 460 " --> pdb=" O MET B 408 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS B 410 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA B 462 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN B 412 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY B 464 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 17 removed outlier: 6.554A pdb=" N MET C 51 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C 72 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL C 127 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP C 74 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE C 129 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLU C 76 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N SER C 131 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 172 through 175 removed outlier: 4.197A pdb=" N PHE C 187 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP C 188 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA C 207 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 190 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL C 205 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA C 192 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR C 546 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 358 through 362 removed outlier: 6.338A pdb=" N GLN C 380 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 388 " --> pdb=" O ALA C 455 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N MET C 408 " --> pdb=" O GLN C 458 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N SER C 460 " --> pdb=" O MET C 408 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS C 410 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA C 462 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASN C 412 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLY C 464 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 499 through 506 removed outlier: 3.677A pdb=" N VAL C 513 " --> pdb=" O VAL C 506 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4641 1.34 - 1.46: 2024 1.46 - 1.58: 7135 1.58 - 1.70: 22 1.70 - 1.82: 89 Bond restraints: 13911 Sorted by residual: bond pdb=" N PHE B 11 " pdb=" CA PHE B 11 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.72e+00 bond pdb=" N VAL B 10 " pdb=" CA VAL B 10 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.37e-02 5.33e+03 6.31e+00 bond pdb=" N GLY C 498 " pdb=" CA GLY C 498 " ideal model delta sigma weight residual 1.449 1.475 -0.026 1.08e-02 8.57e+03 5.78e+00 bond pdb=" N MET C 497 " pdb=" CA MET C 497 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.46e+00 bond pdb=" N GLU C 77 " pdb=" CA GLU C 77 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.30e-02 5.92e+03 4.22e+00 ... (remaining 13906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 18407 1.54 - 3.09: 437 3.09 - 4.63: 74 4.63 - 6.17: 23 6.17 - 7.71: 4 Bond angle restraints: 18945 Sorted by residual: angle pdb=" O4' U D 2 " pdb=" C1' U D 2 " pdb=" N1 U D 2 " ideal model delta sigma weight residual 108.50 111.13 -2.63 7.00e-01 2.04e+00 1.41e+01 angle pdb=" CA GLY C 498 " pdb=" C GLY C 498 " pdb=" O GLY C 498 " ideal model delta sigma weight residual 122.39 118.18 4.21 1.25e+00 6.40e-01 1.14e+01 angle pdb=" CA GLU C 77 " pdb=" C GLU C 77 " pdb=" O GLU C 77 " ideal model delta sigma weight residual 122.41 118.44 3.97 1.21e+00 6.83e-01 1.07e+01 angle pdb=" O5' U F 2 " pdb=" C5' U F 2 " pdb=" C4' U F 2 " ideal model delta sigma weight residual 109.40 111.89 -2.49 8.00e-01 1.56e+00 9.71e+00 angle pdb=" O5' U G 3 " pdb=" C5' U G 3 " pdb=" C4' U G 3 " ideal model delta sigma weight residual 109.40 111.85 -2.45 8.00e-01 1.56e+00 9.41e+00 ... (remaining 18940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 8061 34.83 - 69.67: 370 69.67 - 104.50: 26 104.50 - 139.34: 0 139.34 - 174.17: 2 Dihedral angle restraints: 8459 sinusoidal: 3401 harmonic: 5058 Sorted by residual: dihedral pdb=" O4' U D 2 " pdb=" C1' U D 2 " pdb=" N1 U D 2 " pdb=" C2 U D 2 " ideal model delta sinusoidal sigma weight residual -160.00 -11.10 -148.90 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' U E 6 " pdb=" C1' U E 6 " pdb=" N1 U E 6 " pdb=" C2 U E 6 " ideal model delta sinusoidal sigma weight residual 232.00 57.83 174.17 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C3' U D 1 " pdb=" C4' U D 1 " pdb=" O4' U D 1 " pdb=" C1' U D 1 " ideal model delta sinusoidal sigma weight residual 20.00 -4.89 24.89 1 8.00e+00 1.56e-02 1.39e+01 ... (remaining 8456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2059 0.089 - 0.178: 173 0.178 - 0.267: 3 0.267 - 0.356: 1 0.356 - 0.446: 1 Chirality restraints: 2237 Sorted by residual: chirality pdb=" P U D 2 " pdb=" OP1 U D 2 " pdb=" OP2 U D 2 " pdb=" O5' U D 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CB ILE A 6 " pdb=" CA ILE A 6 " pdb=" CG1 ILE A 6 " pdb=" CG2 ILE A 6 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' U D 2 " pdb=" C4' U D 2 " pdb=" O3' U D 2 " pdb=" C2' U D 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2234 not shown) Planarity restraints: 2462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 61 " -0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO B 62 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 173 " -0.014 2.00e-02 2.50e+03 1.38e-02 4.78e+00 pdb=" CG TRP B 173 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 173 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 173 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 173 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 173 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 173 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 173 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 173 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 490 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 491 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 491 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 491 " -0.026 5.00e-02 4.00e+02 ... (remaining 2459 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1431 2.75 - 3.28: 13737 3.28 - 3.82: 22578 3.82 - 4.36: 25675 4.36 - 4.90: 45458 Nonbonded interactions: 108879 Sorted by model distance: nonbonded pdb=" O SER C 470 " pdb=" OG SER C 473 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A 411 " pdb=" OG1 THR A 469 " model vdw 2.223 3.040 nonbonded pdb=" N GLU A 226 " pdb=" OE1 GLU A 226 " model vdw 2.223 3.120 nonbonded pdb=" O HIS B 344 " pdb=" ND1 HIS B 344 " model vdw 2.225 3.120 nonbonded pdb=" O LEU A 111 " pdb=" OG SER A 114 " model vdw 2.235 3.040 ... (remaining 108874 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 6 through 596) selection = (chain 'B' and resid 6 through 596) selection = (chain 'C' and resid 6 through 596) } ncs_group { reference = (chain 'D' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name O2' or name C1' or name N1 or name C2 or \ name O2 or name N3 or name C4 or name O4 or name C5 or name C6 )) or resid 2 thr \ ough 3)) selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.840 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.080 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.003 0.036 13911 Z= 0.146 Angle : 0.590 7.714 18945 Z= 0.322 Chirality : 0.046 0.446 2237 Planarity : 0.004 0.094 2462 Dihedral : 18.728 174.171 5213 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.33 % Rotamer: Outliers : 0.57 % Allowed : 35.72 % Favored : 63.71 % 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: 0.35 (0.21), residues: 1776 helix: 1.68 (0.22), residues: 551 sheet: -0.04 (0.24), residues: 426 loop : -0.58 (0.24), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 517 TYR 0.012 0.001 TYR B 80 PHE 0.015 0.001 PHE C 531 TRP 0.033 0.004 TRP B 173 HIS 0.001 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (13911) covalent geometry : angle 0.58998 / 0.32 (18945) hydrogen bonds : bond 0.13016 / 8.71 ( 676) hydrogen bonds : angle 5.77728 / 4.02 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.525 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 189 average time/residue: 0.1113 time to fit residues: 32.0562 Evaluate side-chains 178 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 466 ASN Chi-restraints excluded: chain B residue 189 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.0570 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 2.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN C 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117552 restraints weight = 17614.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120181 restraints weight = 13005.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121453 restraints weight = 10626.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.122174 restraints weight = 8801.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122374 restraints weight = 8370.463| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13911 Z= 0.160 Angle : 0.569 7.127 18945 Z= 0.293 Chirality : 0.044 0.272 2237 Planarity : 0.005 0.059 2462 Dihedral : 10.372 175.183 2146 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 4.97 % Allowed : 33.17 % Favored : 61.86 % 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: 0.29 (0.21), residues: 1776 helix: 1.43 (0.22), residues: 565 sheet: -0.06 (0.24), residues: 436 loop : -0.50 (0.25), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 329 TYR 0.011 0.001 TYR C 45 PHE 0.012 0.001 PHE A 416 TRP 0.015 0.002 TRP B 173 HIS 0.002 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (13911) covalent geometry : angle 0.56883 / 0.29 (18945) hydrogen bonds : bond 0.04214 / 2.75 ( 676) hydrogen bonds : angle 4.95220 / 3.46 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 181 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7445 (ptp90) cc_final: 0.7226 (ptp-110) REVERT: A 420 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: C 379 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8228 (m) outliers start: 70 outliers final: 44 residues processed: 229 average time/residue: 0.1040 time to fit residues: 36.8544 Evaluate side-chains 218 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 101 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 21 optimal weight: 0.0170 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN B 549 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.153358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123785 restraints weight = 17146.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125953 restraints weight = 12290.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127512 restraints weight = 10471.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128384 restraints weight = 8343.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128861 restraints weight = 7767.148| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13911 Z= 0.167 Angle : 0.563 6.770 18945 Z= 0.289 Chirality : 0.044 0.273 2237 Planarity : 0.004 0.046 2462 Dihedral : 10.265 175.325 2144 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.67 % Favored : 95.16 % Rotamer: Outliers : 6.89 % Allowed : 30.97 % Favored : 62.14 % 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 (0.21), residues: 1776 helix: 1.46 (0.22), residues: 565 sheet: -0.04 (0.24), residues: 437 loop : -0.50 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.013 0.001 TYR C 411 PHE 0.014 0.001 PHE A 416 TRP 0.011 0.002 TRP B 173 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (13911) covalent geometry : angle 0.56292 / 0.29 (18945) hydrogen bonds : bond 0.03953 / 2.56 ( 676) hydrogen bonds : angle 4.80378 / 3.36 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 183 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7389 (ptp90) cc_final: 0.7117 (ptp-110) REVERT: A 420 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: A 577 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8530 (mt) REVERT: B 312 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6114 (ttp80) REVERT: B 473 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8575 (p) REVERT: C 53 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9168 (tp) REVERT: C 189 MET cc_start: 0.8033 (mmm) cc_final: 0.7817 (mmm) REVERT: C 202 ILE cc_start: 0.8502 (mm) cc_final: 0.8077 (mm) REVERT: C 379 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8214 (m) outliers start: 97 outliers final: 55 residues processed: 253 average time/residue: 0.1049 time to fit residues: 41.2212 Evaluate side-chains 228 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 ASN B 61 ASN B 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.145968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115626 restraints weight = 17791.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116360 restraints weight = 13710.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117797 restraints weight = 12095.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119544 restraints weight = 9959.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119620 restraints weight = 8642.940| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13911 Z= 0.214 Angle : 0.607 12.793 18945 Z= 0.309 Chirality : 0.046 0.272 2237 Planarity : 0.004 0.047 2462 Dihedral : 10.205 174.705 2141 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 7.95 % Allowed : 30.47 % Favored : 61.58 % 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: 0.19 (0.21), residues: 1776 helix: 1.35 (0.22), residues: 563 sheet: -0.09 (0.24), residues: 435 loop : -0.57 (0.25), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 517 TYR 0.017 0.002 TYR C 411 PHE 0.015 0.002 PHE A 416 TRP 0.043 0.005 TRP B 173 HIS 0.003 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (13911) covalent geometry : angle 0.60668 / 0.31 (18945) hydrogen bonds : bond 0.04086 / 2.65 ( 676) hydrogen bonds : angle 4.85989 / 3.41 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 177 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: A 577 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8504 (mt) REVERT: B 173 TRP cc_start: 0.8304 (m-10) cc_final: 0.8034 (m-10) REVERT: B 292 ILE cc_start: 0.3596 (OUTLIER) cc_final: 0.3345 (mp) REVERT: B 312 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6204 (ttp80) REVERT: B 473 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8613 (p) REVERT: C 8 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5563 (mp0) REVERT: C 53 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9198 (tp) REVERT: C 202 ILE cc_start: 0.8489 (mm) cc_final: 0.8012 (mm) outliers start: 112 outliers final: 73 residues processed: 265 average time/residue: 0.0891 time to fit residues: 36.3108 Evaluate side-chains 247 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 167 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 123 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 159 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116144 restraints weight = 17815.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116350 restraints weight = 14295.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.118163 restraints weight = 12211.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119531 restraints weight = 9877.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119673 restraints weight = 9014.591| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13911 Z= 0.192 Angle : 0.595 12.526 18945 Z= 0.302 Chirality : 0.045 0.324 2237 Planarity : 0.004 0.048 2462 Dihedral : 10.159 174.814 2141 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.01 % Favored : 94.82 % Rotamer: Outliers : 7.32 % Allowed : 30.82 % Favored : 61.86 % 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: 0.18 (0.21), residues: 1776 helix: 1.34 (0.22), residues: 563 sheet: -0.14 (0.24), residues: 436 loop : -0.55 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 84 TYR 0.015 0.001 TYR C 411 PHE 0.014 0.001 PHE B 416 TRP 0.019 0.003 TRP B 173 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (13911) covalent geometry : angle 0.59517 / 0.30 (18945) hydrogen bonds : bond 0.03940 / 2.56 ( 676) hydrogen bonds : angle 4.80425 / 3.37 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 179 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: A 577 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8541 (mt) REVERT: B 173 TRP cc_start: 0.8316 (m100) cc_final: 0.8054 (m-10) REVERT: B 222 GLN cc_start: 0.7847 (pp30) cc_final: 0.7251 (pt0) REVERT: B 292 ILE cc_start: 0.3536 (OUTLIER) cc_final: 0.3318 (mp) REVERT: B 312 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6244 (ttp80) REVERT: B 355 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6720 (mp) REVERT: B 473 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8618 (p) REVERT: C 8 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5553 (mp0) REVERT: C 53 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9172 (tp) REVERT: C 202 ILE cc_start: 0.8480 (mm) cc_final: 0.8255 (mm) REVERT: C 344 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.5861 (t70) REVERT: C 379 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8305 (m) REVERT: C 534 MET cc_start: 0.7211 (tmm) cc_final: 0.6980 (tmm) outliers start: 103 outliers final: 77 residues processed: 259 average time/residue: 0.0953 time to fit residues: 38.0858 Evaluate side-chains 254 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 167 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 154 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.153354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.124225 restraints weight = 17240.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.125080 restraints weight = 13168.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126344 restraints weight = 10593.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.127714 restraints weight = 9514.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127846 restraints weight = 8568.201| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13911 Z= 0.160 Angle : 0.579 11.600 18945 Z= 0.293 Chirality : 0.045 0.294 2237 Planarity : 0.004 0.047 2462 Dihedral : 10.086 175.440 2141 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 7.95 % Allowed : 30.26 % Favored : 61.79 % 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: 0.19 (0.21), residues: 1776 helix: 1.40 (0.22), residues: 564 sheet: -0.06 (0.24), residues: 429 loop : -0.64 (0.25), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 84 TYR 0.012 0.001 TYR C 411 PHE 0.017 0.001 PHE C 452 TRP 0.017 0.003 TRP B 173 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (13911) covalent geometry : angle 0.57855 / 0.29 (18945) hydrogen bonds : bond 0.03743 / 2.43 ( 676) hydrogen bonds : angle 4.71929 / 3.31 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 186 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7479 (mmm160) cc_final: 0.7273 (mmm160) REVERT: A 420 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 577 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8540 (mt) REVERT: B 173 TRP cc_start: 0.8370 (m100) cc_final: 0.8087 (m-10) REVERT: B 222 GLN cc_start: 0.7834 (pp30) cc_final: 0.7216 (pt0) REVERT: B 312 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6273 (ttp80) REVERT: B 335 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8468 (mm) REVERT: B 355 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6669 (mp) REVERT: B 473 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8656 (p) REVERT: C 53 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9180 (tp) REVERT: C 54 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.9081 (p) REVERT: C 202 ILE cc_start: 0.8430 (mm) cc_final: 0.8189 (mm) REVERT: C 344 HIS cc_start: 0.6762 (OUTLIER) cc_final: 0.5848 (t70) REVERT: C 379 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8273 (m) REVERT: C 534 MET cc_start: 0.7193 (tmm) cc_final: 0.6933 (tmm) outliers start: 112 outliers final: 84 residues processed: 271 average time/residue: 0.1023 time to fit residues: 42.6284 Evaluate side-chains 267 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 173 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 chunk 43 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.147049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117765 restraints weight = 17560.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118342 restraints weight = 13577.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.119859 restraints weight = 11587.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122288 restraints weight = 9585.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.122247 restraints weight = 8038.114| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 13911 Z= 0.271 Angle : 0.659 11.665 18945 Z= 0.337 Chirality : 0.048 0.343 2237 Planarity : 0.005 0.048 2462 Dihedral : 10.190 174.575 2141 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.57 % Favored : 94.26 % Rotamer: Outliers : 8.66 % Allowed : 30.40 % Favored : 60.94 % 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: 0.03 (0.21), residues: 1776 helix: 1.20 (0.22), residues: 564 sheet: -0.20 (0.24), residues: 435 loop : -0.66 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 84 TYR 0.021 0.002 TYR C 411 PHE 0.020 0.002 PHE B 416 TRP 0.018 0.003 TRP B 173 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.27 (13911) covalent geometry : angle 0.65876 / 0.34 (18945) hydrogen bonds : bond 0.04355 / 2.83 ( 676) hydrogen bonds : angle 4.91854 / 3.46 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 176 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7245 (mmm160) REVERT: A 420 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: A 577 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 173 TRP cc_start: 0.8469 (m100) cc_final: 0.8103 (m-10) REVERT: B 222 GLN cc_start: 0.7891 (pp30) cc_final: 0.7271 (pt0) REVERT: B 292 ILE cc_start: 0.3662 (OUTLIER) cc_final: 0.3438 (mp) REVERT: B 312 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6313 (ttp80) REVERT: B 355 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6938 (mp) REVERT: B 473 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8694 (p) REVERT: C 53 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9204 (tp) REVERT: C 202 ILE cc_start: 0.8480 (mm) cc_final: 0.8071 (mm) REVERT: C 344 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.5932 (t70) REVERT: C 534 MET cc_start: 0.7197 (tmm) cc_final: 0.6935 (tmm) outliers start: 122 outliers final: 95 residues processed: 273 average time/residue: 0.1034 time to fit residues: 42.5816 Evaluate side-chains 270 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 167 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 81 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 66 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.149076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118778 restraints weight = 17516.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119609 restraints weight = 13574.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121480 restraints weight = 11727.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122362 restraints weight = 9431.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122619 restraints weight = 8633.454| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13911 Z= 0.122 Angle : 0.576 10.916 18945 Z= 0.292 Chirality : 0.044 0.272 2237 Planarity : 0.004 0.048 2462 Dihedral : 9.990 176.142 2141 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.61 % Rotamer: Outliers : 6.53 % Allowed : 32.53 % Favored : 60.94 % 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: 0.22 (0.21), residues: 1776 helix: 1.44 (0.22), residues: 564 sheet: -0.08 (0.24), residues: 433 loop : -0.63 (0.25), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.014 0.001 TYR A 411 PHE 0.017 0.001 PHE C 531 TRP 0.018 0.003 TRP B 173 HIS 0.002 0.000 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13911) covalent geometry : angle 0.57576 / 0.29 (18945) hydrogen bonds : bond 0.03546 / 2.30 ( 676) hydrogen bonds : angle 4.65741 / 3.26 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 187 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8156 (mmm) cc_final: 0.7775 (tpp) REVERT: A 356 ARG cc_start: 0.7528 (mmm160) cc_final: 0.7246 (mmm160) REVERT: A 420 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: B 173 TRP cc_start: 0.8405 (m100) cc_final: 0.8094 (m-10) REVERT: B 222 GLN cc_start: 0.7807 (pp30) cc_final: 0.7205 (pt0) REVERT: B 312 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6258 (ttp80) REVERT: B 335 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8394 (mm) REVERT: B 473 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8617 (p) REVERT: C 53 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9146 (tp) REVERT: C 202 ILE cc_start: 0.8350 (mm) cc_final: 0.8099 (mm) REVERT: C 344 HIS cc_start: 0.6700 (OUTLIER) cc_final: 0.5790 (t70) REVERT: C 379 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8231 (m) REVERT: C 534 MET cc_start: 0.7128 (tmm) cc_final: 0.6889 (tmm) outliers start: 92 outliers final: 73 residues processed: 257 average time/residue: 0.0982 time to fit residues: 38.7564 Evaluate side-chains 257 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 167 optimal weight: 0.4980 chunk 154 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.146385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116135 restraints weight = 17871.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.116431 restraints weight = 14137.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117834 restraints weight = 12419.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119977 restraints weight = 10519.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.120087 restraints weight = 8964.627| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13911 Z= 0.175 Angle : 0.599 10.153 18945 Z= 0.304 Chirality : 0.045 0.271 2237 Planarity : 0.004 0.047 2462 Dihedral : 9.981 176.229 2141 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.01 % Favored : 94.82 % Rotamer: Outliers : 6.25 % Allowed : 32.46 % Favored : 61.29 % 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: 0.21 (0.21), residues: 1776 helix: 1.40 (0.22), residues: 564 sheet: -0.04 (0.24), residues: 429 loop : -0.63 (0.25), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 84 TYR 0.014 0.001 TYR C 411 PHE 0.017 0.001 PHE B 416 TRP 0.016 0.003 TRP B 173 HIS 0.002 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (13911) covalent geometry : angle 0.59938 / 0.30 (18945) hydrogen bonds : bond 0.03721 / 2.42 ( 676) hydrogen bonds : angle 4.68987 / 3.29 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 177 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 264 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.6883 (t80) REVERT: A 356 ARG cc_start: 0.7466 (mmm160) cc_final: 0.7160 (mmm160) REVERT: A 420 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: B 77 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: B 173 TRP cc_start: 0.8415 (m100) cc_final: 0.8103 (m-10) REVERT: B 222 GLN cc_start: 0.7801 (pp30) cc_final: 0.7192 (pt0) REVERT: B 292 ILE cc_start: 0.3668 (OUTLIER) cc_final: 0.3460 (mp) REVERT: B 312 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6254 (ttp80) REVERT: B 473 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8629 (p) REVERT: C 53 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9155 (tp) REVERT: C 202 ILE cc_start: 0.8391 (mm) cc_final: 0.8139 (mm) REVERT: C 344 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.5850 (t70) REVERT: C 379 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8305 (m) REVERT: C 534 MET cc_start: 0.7120 (tmm) cc_final: 0.6895 (tmm) outliers start: 88 outliers final: 75 residues processed: 245 average time/residue: 0.1112 time to fit residues: 41.3971 Evaluate side-chains 258 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 174 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 161 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 124 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117652 restraints weight = 17604.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119229 restraints weight = 13064.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.120734 restraints weight = 11221.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121819 restraints weight = 9209.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.121949 restraints weight = 8443.015| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13911 Z= 0.146 Angle : 0.579 8.442 18945 Z= 0.294 Chirality : 0.044 0.271 2237 Planarity : 0.004 0.048 2462 Dihedral : 9.903 176.730 2141 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.05 % Rotamer: Outliers : 6.11 % Allowed : 32.67 % Favored : 61.22 % 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: 0.26 (0.21), residues: 1776 helix: 1.46 (0.22), residues: 564 sheet: -0.08 (0.24), residues: 436 loop : -0.55 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 112 TYR 0.012 0.001 TYR C 45 PHE 0.016 0.001 PHE B 416 TRP 0.018 0.003 TRP B 173 HIS 0.002 0.000 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (13911) covalent geometry : angle 0.57865 / 0.29 (18945) hydrogen bonds : bond 0.03569 / 2.31 ( 676) hydrogen bonds : angle 4.62574 / 3.24 ( 1881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 178 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 264 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6866 (t80) REVERT: A 356 ARG cc_start: 0.7438 (mmm160) cc_final: 0.7145 (mmm160) REVERT: A 420 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: B 77 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7573 (pt0) REVERT: B 138 TYR cc_start: 0.8322 (p90) cc_final: 0.8010 (p90) REVERT: B 173 TRP cc_start: 0.8410 (m100) cc_final: 0.8180 (m-10) REVERT: B 222 GLN cc_start: 0.7761 (pp30) cc_final: 0.7165 (pt0) REVERT: B 292 ILE cc_start: 0.3692 (OUTLIER) cc_final: 0.3486 (mp) REVERT: B 312 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6229 (ttp80) REVERT: B 473 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8607 (p) REVERT: C 53 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9150 (tp) REVERT: C 202 ILE cc_start: 0.8365 (mm) cc_final: 0.8113 (mm) REVERT: C 344 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.5814 (t70) REVERT: C 379 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8283 (m) REVERT: C 534 MET cc_start: 0.7126 (tmm) cc_final: 0.6884 (tmm) outliers start: 86 outliers final: 76 residues processed: 244 average time/residue: 0.1097 time to fit residues: 40.9030 Evaluate side-chains 263 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 178 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 148 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.145140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114632 restraints weight = 17991.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115295 restraints weight = 14215.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116524 restraints weight = 12348.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117758 restraints weight = 10618.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117995 restraints weight = 9458.051| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13911 Z= 0.213 Angle : 0.631 10.199 18945 Z= 0.320 Chirality : 0.046 0.274 2237 Planarity : 0.004 0.050 2462 Dihedral : 9.951 176.070 2141 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 6.68 % Allowed : 32.03 % Favored : 61.29 % 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: 0.16 (0.21), residues: 1776 helix: 1.34 (0.22), residues: 565 sheet: -0.14 (0.24), residues: 436 loop : -0.60 (0.25), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 84 TYR 0.017 0.002 TYR C 411 PHE 0.018 0.002 PHE C 531 TRP 0.019 0.003 TRP B 173 HIS 0.003 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.21 (13911) covalent geometry : angle 0.63136 / 0.32 (18945) hydrogen bonds : bond 0.03952 / 2.56 ( 676) hydrogen bonds : angle 4.75811 / 3.35 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2098.16 seconds wall clock time: 37 minutes 5.40 seconds (2225.40 seconds total)