Starting phenix.real_space_refine on Fri Jul 3 09:39:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx0_37896/07_2026/8wx0_37896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx0_37896/07_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_37896/07_2026/8wx0_37896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx0_37896/07_2026/8wx0_37896.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx0_37896/07_2026/8wx0_37896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx0_37896/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.46, per 1000 atoms: 0.25 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: 1.34 Conformation dependent library (CDL) restraints added in 641.6 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: 0.39 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: 2.54 Time building geometry restraints manager: 1.72 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: 18435 1.54 - 3.09: 408 3.09 - 4.63: 75 4.63 - 6.17: 23 6.17 - 7.71: 4 Bond angle restraints: 18945 Sorted by residual: 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=" N THR B 316 " pdb=" CA THR B 316 " pdb=" C THR B 316 " ideal model delta sigma weight residual 114.56 110.91 3.65 1.27e+00 6.20e-01 8.25e+00 angle pdb=" C VAL C 510 " pdb=" N ASP C 511 " pdb=" CA ASP C 511 " ideal model delta sigma weight residual 121.54 126.96 -5.42 1.91e+00 2.74e-01 8.05e+00 angle pdb=" N1 U E 6 " pdb=" C2 U E 6 " pdb=" O2 U E 6 " ideal model delta sigma weight residual 122.80 124.78 -1.98 7.00e-01 2.04e+00 8.04e+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: 2068 0.089 - 0.178: 164 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: 1.250 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.170 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- 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= 0.145 Angle : 0.583 7.714 18945 Z= 0.312 Chirality : 0.045 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 0.58289 / 0.31 (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 : 0.434 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 189 average time/residue: 0.1082 time to fit residues: 31.0469 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 : 0.528 ------------------------------------------------------------------------------- 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 = 0.148336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117514 restraints weight = 17616.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120164 restraints weight = 13010.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121418 restraints weight = 10657.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121954 restraints weight = 8867.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.122247 restraints weight = 8435.553| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 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: 0.0522 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= 0.161 Angle : 0.569 7.201 18945 Z= 0.294 Chirality : 0.044 0.272 2237 Planarity : 0.005 0.059 2462 Dihedral : 10.402 175.593 2146 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 4.90 % Allowed : 33.24 % 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: -0.05 (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 350 TYR 0.011 0.001 TYR C 45 PHE 0.013 0.001 PHE C 536 TRP 0.015 0.002 TRP B 173 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (13911) covalent geometry : angle 0.56919 / 0.29 (18945) hydrogen bonds : bond 0.04142 / 2.70 ( 676) hydrogen bonds : angle 4.95689 / 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 250 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 181 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7448 (ptp90) cc_final: 0.7222 (ptp-110) REVERT: A 420 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: C 379 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8231 (m) outliers start: 69 outliers final: 44 residues processed: 228 average time/residue: 0.0903 time to fit residues: 31.8172 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 : 0.494 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 21 optimal weight: 0.0570 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.5502 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.153446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123849 restraints weight = 17135.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.126028 restraints weight = 12304.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127604 restraints weight = 10509.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.128525 restraints weight = 8374.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128911 restraints weight = 7783.018| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 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 = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13911 Z= 0.167 Angle : 0.563 6.467 18945 Z= 0.289 Chirality : 0.044 0.273 2237 Planarity : 0.004 0.046 2462 Dihedral : 10.304 175.448 2144 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.21 % Rotamer: Outliers : 6.39 % Allowed : 31.61 % Favored : 62.00 % 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: 0.31 (0.21), residues: 1776 helix: 1.47 (0.22), residues: 563 sheet: -0.04 (0.24), residues: 437 loop : -0.52 (0.25), residues: 776 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 A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (13911) covalent geometry : angle 0.56264 / 0.29 (18945) hydrogen bonds : bond 0.03943 / 2.56 ( 676) hydrogen bonds : angle 4.82929 / 3.38 ( 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 272 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 182 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7395 (ptp90) cc_final: 0.7128 (ptp-110) REVERT: A 420 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: A 577 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8526 (mt) REVERT: B 312 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6145 (ttp80) REVERT: B 473 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8590 (p) REVERT: C 53 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9184 (tp) REVERT: C 202 ILE cc_start: 0.8528 (mm) cc_final: 0.8144 (mm) REVERT: C 379 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8233 (m) outliers start: 90 outliers final: 52 residues processed: 244 average time/residue: 0.0934 time to fit residues: 34.8616 Evaluate side-chains 221 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 286 LEU Chi-restraints excluded: chain B residue 312 ARG 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 473 SER 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 331 LEU 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 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: 5.9990 chunk 96 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 173 optimal weight: 8.9990 chunk 42 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.145728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115738 restraints weight = 17797.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116102 restraints weight = 14168.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117632 restraints weight = 12175.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.118790 restraints weight = 10347.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118971 restraints weight = 8867.140| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 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 (9 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 13911 Z= 0.243 Angle : 0.617 7.730 18945 Z= 0.318 Chirality : 0.046 0.272 2237 Planarity : 0.005 0.048 2462 Dihedral : 10.278 174.913 2141 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 8.10 % Allowed : 30.26 % Favored : 61.65 % 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: 1.31 (0.22), residues: 563 sheet: -0.09 (0.24), residues: 435 loop : -0.60 (0.25), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.019 0.002 TYR C 411 PHE 0.016 0.002 PHE A 416 TRP 0.024 0.003 TRP B 173 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (13911) covalent geometry : angle 0.61706 / 0.32 (18945) hydrogen bonds : bond 0.04226 / 2.73 ( 676) hydrogen bonds : angle 4.91571 / 3.46 ( 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 288 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 174 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7498 (ptp90) cc_final: 0.7217 (ptp-110) REVERT: A 420 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: A 577 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8491 (mt) REVERT: B 292 ILE cc_start: 0.3554 (OUTLIER) cc_final: 0.3297 (mp) REVERT: B 312 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6227 (ttp80) REVERT: B 473 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8648 (p) REVERT: C 8 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5552 (mp0) REVERT: C 53 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9218 (tp) REVERT: C 202 ILE cc_start: 0.8503 (mm) cc_final: 0.8043 (mm) outliers start: 114 outliers final: 79 residues processed: 262 average time/residue: 0.1091 time to fit residues: 43.4316 Evaluate side-chains 253 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 167 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 189 MET 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 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 501 SER 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 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 445 VAL 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 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 243 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 123 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN ** 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 = 0.3653 r_free = 0.3653 target = 0.150512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.121051 restraints weight = 17371.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.123837 restraints weight = 12411.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124924 restraints weight = 10138.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125718 restraints weight = 8308.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125989 restraints weight = 7785.811| |-----------------------------------------------------------------------------| 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: 0.8286 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 13911 Z= 0.258 Angle : 0.637 7.220 18945 Z= 0.328 Chirality : 0.047 0.275 2237 Planarity : 0.005 0.049 2462 Dihedral : 10.314 174.868 2141 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 8.38 % Allowed : 29.97 % Favored : 61.65 % 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: 0.02 (0.21), residues: 1776 helix: 1.20 (0.22), residues: 563 sheet: -0.19 (0.24), residues: 435 loop : -0.67 (0.24), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.020 0.002 TYR C 411 PHE 0.016 0.002 PHE A 416 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 0.00617 / 0.26 (13911) covalent geometry : angle 0.63666 / 0.33 (18945) hydrogen bonds : bond 0.04331 / 2.81 ( 676) hydrogen bonds : angle 4.94972 / 3.48 ( 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 293 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 175 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: A 577 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8532 (mt) REVERT: B 222 GLN cc_start: 0.7842 (pp30) cc_final: 0.7220 (pt0) REVERT: B 292 ILE cc_start: 0.3658 (OUTLIER) cc_final: 0.3431 (mp) REVERT: B 312 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6178 (ttp80) REVERT: B 355 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6780 (mp) REVERT: C 8 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.5588 (mp0) REVERT: C 53 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9217 (tp) REVERT: C 202 ILE cc_start: 0.8496 (mm) cc_final: 0.8113 (mm) REVERT: C 344 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.5907 (t70) REVERT: C 497 MET cc_start: 0.8556 (mmm) cc_final: 0.8281 (mmm) outliers start: 118 outliers final: 90 residues processed: 267 average time/residue: 0.1089 time to fit residues: 44.1907 Evaluate side-chains 261 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 163 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 233 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 501 SER 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 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 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 335 LEU Chi-restraints excluded: chain B residue 350 ARG 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 386 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 465 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 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 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 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: 6.9990 chunk 162 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 36 optimal weight: 0.0970 overall best weight: 1.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118283 restraints weight = 17653.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.118812 restraints weight = 13513.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120323 restraints weight = 11680.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122393 restraints weight = 9813.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122502 restraints weight = 8357.153| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 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 = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13911 Z= 0.128 Angle : 0.567 14.163 18945 Z= 0.287 Chirality : 0.044 0.274 2237 Planarity : 0.004 0.048 2462 Dihedral : 10.113 175.658 2141 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.61 % Rotamer: Outliers : 6.61 % Allowed : 31.75 % Favored : 61.65 % 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: 1.48 (0.22), residues: 564 sheet: -0.16 (0.24), residues: 440 loop : -0.59 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.013 0.001 TYR A 411 PHE 0.019 0.001 PHE C 452 TRP 0.014 0.002 TRP B 173 HIS 0.002 0.000 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13911) covalent geometry : angle 0.56710 / 0.29 (18945) hydrogen bonds : bond 0.03628 / 2.35 ( 676) hydrogen bonds : angle 4.70975 / 3.30 ( 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 279 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 186 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: B 222 GLN cc_start: 0.7776 (pp30) cc_final: 0.7163 (pt0) REVERT: B 312 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6143 (ttp80) REVERT: B 335 LEU cc_start: 0.8738 (mm) cc_final: 0.8462 (mm) REVERT: B 483 ASN cc_start: 0.8549 (t0) cc_final: 0.8347 (t0) REVERT: C 8 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.5600 (mp0) REVERT: C 53 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9158 (tp) REVERT: C 188 ASP cc_start: 0.8357 (t0) cc_final: 0.8128 (t0) REVERT: C 202 ILE cc_start: 0.8378 (mm) cc_final: 0.8145 (mm) REVERT: C 344 HIS cc_start: 0.6721 (OUTLIER) cc_final: 0.5795 (t70) REVERT: C 379 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8210 (m) REVERT: C 497 MET cc_start: 0.8438 (mmm) cc_final: 0.8220 (mmm) REVERT: C 534 MET cc_start: 0.7230 (tmm) cc_final: 0.6925 (tmm) outliers start: 93 outliers final: 69 residues processed: 256 average time/residue: 0.1092 time to fit residues: 42.5082 Evaluate side-chains 248 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 173 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 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 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 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 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 331 LEU Chi-restraints excluded: chain B residue 362 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 418 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 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 8 GLU 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 200 VAL Chi-restraints excluded: chain C residue 208 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 549 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.145208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114701 restraints weight = 17867.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115281 restraints weight = 14975.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116045 restraints weight = 13153.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117565 restraints weight = 11310.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117776 restraints weight = 9702.005| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 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 = 0.3216 r_free = 0.3216 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: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13911 Z= 0.206 Angle : 0.604 10.657 18945 Z= 0.309 Chirality : 0.045 0.270 2237 Planarity : 0.004 0.048 2462 Dihedral : 10.119 175.381 2141 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 7.53 % Allowed : 30.89 % 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: 0.14 (0.21), residues: 1776 helix: 1.35 (0.22), residues: 564 sheet: -0.13 (0.24), residues: 435 loop : -0.64 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 84 TYR 0.016 0.001 TYR C 411 PHE 0.017 0.002 PHE B 416 TRP 0.014 0.002 TRP B 173 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (13911) covalent geometry : angle 0.60415 / 0.31 (18945) hydrogen bonds : bond 0.03915 / 2.54 ( 676) hydrogen bonds : angle 4.77679 / 3.36 ( 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 282 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 176 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7269 (ptp-110) cc_final: 0.7027 (ptp-110) REVERT: A 420 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: B 61 ASN cc_start: 0.8033 (m-40) cc_final: 0.6976 (p0) REVERT: B 222 GLN cc_start: 0.7804 (pp30) cc_final: 0.7195 (pt0) REVERT: B 312 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6270 (ttp80) REVERT: B 355 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6738 (mp) REVERT: C 52 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9108 (pp) REVERT: C 53 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9195 (tp) REVERT: C 202 ILE cc_start: 0.8434 (mm) cc_final: 0.8224 (mm) REVERT: C 344 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.5854 (t70) outliers start: 106 outliers final: 82 residues processed: 260 average time/residue: 0.1073 time to fit residues: 42.8028 Evaluate side-chains 258 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 170 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 166 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 195 ILE 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 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 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 501 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 57 THR Chi-restraints excluded: chain B residue 72 THR 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 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 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 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 562 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain C residue 52 LEU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 81 optimal weight: 0.0370 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115375 restraints weight = 17801.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115030 restraints weight = 14552.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.116370 restraints weight = 12645.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117949 restraints weight = 10846.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118057 restraints weight = 9499.244| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13911 Z= 0.179 Angle : 0.593 10.819 18945 Z= 0.303 Chirality : 0.045 0.272 2237 Planarity : 0.004 0.048 2462 Dihedral : 10.068 175.592 2141 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer: Outliers : 7.74 % Allowed : 31.04 % 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: 0.14 (0.21), residues: 1776 helix: 1.32 (0.22), residues: 564 sheet: -0.15 (0.24), residues: 435 loop : -0.61 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 84 TYR 0.014 0.001 TYR C 411 PHE 0.019 0.002 PHE C 531 TRP 0.040 0.005 TRP B 173 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (13911) covalent geometry : angle 0.59291 / 0.30 (18945) hydrogen bonds : bond 0.03826 / 2.49 ( 676) hydrogen bonds : angle 4.76125 / 3.35 ( 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 283 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 174 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 533 ASP cc_start: 0.7116 (m-30) cc_final: 0.6718 (m-30) REVERT: B 61 ASN cc_start: 0.8028 (m-40) cc_final: 0.6979 (p0) REVERT: B 222 GLN cc_start: 0.7758 (pp30) cc_final: 0.7157 (pt0) REVERT: B 292 ILE cc_start: 0.3556 (OUTLIER) cc_final: 0.3345 (mp) REVERT: B 312 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6283 (ttp80) REVERT: B 355 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6792 (mp) REVERT: C 53 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9187 (tp) REVERT: C 202 ILE cc_start: 0.8393 (mm) cc_final: 0.8156 (mm) REVERT: C 344 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.5869 (t70) REVERT: C 379 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8321 (m) REVERT: C 497 MET cc_start: 0.8427 (mmm) cc_final: 0.7990 (mmm) REVERT: C 534 MET cc_start: 0.7136 (tmm) cc_final: 0.6934 (tmm) outliers start: 109 outliers final: 90 residues processed: 261 average time/residue: 0.1081 time to fit residues: 42.8443 Evaluate side-chains 266 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 169 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 501 SER 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 590 MET Chi-restraints excluded: chain B residue 31 THR 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 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 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 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 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 514 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 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 200 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 243 LEU 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 584 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 154 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.149491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118966 restraints weight = 17649.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119891 restraints weight = 13901.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121790 restraints weight = 11745.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122474 restraints weight = 9370.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123006 restraints weight = 8895.018| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13911 Z= 0.120 Angle : 0.569 13.028 18945 Z= 0.289 Chirality : 0.044 0.271 2237 Planarity : 0.004 0.048 2462 Dihedral : 9.933 176.733 2141 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.33 % Rotamer: Outliers : 6.18 % Allowed : 32.53 % 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: 0.26 (0.21), residues: 1776 helix: 1.46 (0.22), residues: 564 sheet: -0.12 (0.24), residues: 440 loop : -0.55 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 517 TYR 0.013 0.001 TYR A 411 PHE 0.016 0.001 PHE C 531 TRP 0.039 0.005 TRP B 173 HIS 0.002 0.000 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13911) covalent geometry : angle 0.56902 / 0.29 (18945) hydrogen bonds : bond 0.03447 / 2.23 ( 676) hydrogen bonds : angle 4.62372 / 3.24 ( 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 269 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 182 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 226 GLU cc_start: 0.6948 (mp0) cc_final: 0.6593 (mp0) REVERT: A 264 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6798 (t80) REVERT: A 420 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: A 533 ASP cc_start: 0.6923 (m-30) cc_final: 0.6591 (m-30) REVERT: B 61 ASN cc_start: 0.7974 (m-40) cc_final: 0.6920 (p0) REVERT: B 222 GLN cc_start: 0.7739 (pp30) cc_final: 0.7101 (pt0) REVERT: B 312 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6215 (ttp80) REVERT: C 53 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9161 (tp) REVERT: C 202 ILE cc_start: 0.8262 (mm) cc_final: 0.8013 (mm) REVERT: C 344 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.5788 (t70) REVERT: C 379 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8234 (m) REVERT: C 497 MET cc_start: 0.8349 (mmm) cc_final: 0.8031 (mmm) outliers start: 87 outliers final: 73 residues processed: 249 average time/residue: 0.1077 time to fit residues: 41.3569 Evaluate side-chains 256 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 177 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 263 ASP 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 521 LEU Chi-restraints excluded: chain A residue 550 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 72 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 111 LEU 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 200 VAL 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 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 440 ARG 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 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 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 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 541 THR Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 58 optimal weight: 0.0170 chunk 0 optimal weight: 30.0000 chunk 124 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120883 restraints weight = 17442.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121050 restraints weight = 13599.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122540 restraints weight = 11811.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.123520 restraints weight = 9870.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.124305 restraints weight = 9086.013| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13911 Z= 0.129 Angle : 0.570 11.964 18945 Z= 0.289 Chirality : 0.045 0.337 2237 Planarity : 0.004 0.048 2462 Dihedral : 9.868 177.382 2141 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.62 % Favored : 95.21 % Rotamer: Outliers : 5.82 % Allowed : 32.60 % 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: 0.31 (0.21), residues: 1776 helix: 1.47 (0.22), residues: 565 sheet: -0.02 (0.24), residues: 436 loop : -0.54 (0.25), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 84 TYR 0.012 0.001 TYR A 411 PHE 0.015 0.001 PHE B 416 TRP 0.033 0.004 TRP B 173 HIS 0.002 0.000 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13911) covalent geometry : angle 0.57024 / 0.29 (18945) hydrogen bonds : bond 0.03416 / 2.22 ( 676) hydrogen bonds : angle 4.57887 / 3.21 ( 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 263 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 181 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 264 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.6804 (t80) REVERT: A 420 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: A 533 ASP cc_start: 0.6829 (m-30) cc_final: 0.6505 (m-30) REVERT: B 61 ASN cc_start: 0.7952 (m-40) cc_final: 0.6864 (p0) REVERT: B 222 GLN cc_start: 0.7713 (pp30) cc_final: 0.7081 (pt0) REVERT: B 312 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6282 (ttp80) REVERT: C 53 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9168 (tp) REVERT: C 202 ILE cc_start: 0.8216 (mm) cc_final: 0.7970 (mm) REVERT: C 344 HIS cc_start: 0.6660 (OUTLIER) cc_final: 0.5806 (t70) REVERT: C 379 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8245 (m) REVERT: C 497 MET cc_start: 0.8399 (mmm) cc_final: 0.7976 (mmm) outliers start: 82 outliers final: 69 residues processed: 245 average time/residue: 0.1074 time to fit residues: 40.3195 Evaluate side-chains 251 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 216 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 263 ASP 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 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 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 111 LEU 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 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 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 440 ARG 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 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 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 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 541 THR 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: 7.9990 chunk 125 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 167 optimal weight: 0.0870 chunk 150 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.125167 restraints weight = 17285.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.125640 restraints weight = 13368.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127304 restraints weight = 11146.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129044 restraints weight = 9150.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129189 restraints weight = 7996.329| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13911 Z= 0.130 Angle : 0.567 11.797 18945 Z= 0.287 Chirality : 0.044 0.271 2237 Planarity : 0.004 0.048 2462 Dihedral : 9.797 177.630 2141 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.33 % Rotamer: Outliers : 5.97 % Allowed : 32.46 % 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: 0.34 (0.21), residues: 1776 helix: 1.49 (0.22), residues: 566 sheet: -0.02 (0.24), residues: 437 loop : -0.51 (0.25), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 517 TYR 0.011 0.001 TYR A 411 PHE 0.014 0.001 PHE B 416 TRP 0.031 0.004 TRP B 173 HIS 0.002 0.000 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (13911) covalent geometry : angle 0.56652 / 0.29 (18945) hydrogen bonds : bond 0.03363 / 2.19 ( 676) hydrogen bonds : angle 4.52684 / 3.18 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.74 seconds wall clock time: 37 minutes 58.47 seconds (2278.47 seconds total)