Starting phenix.real_space_refine on Thu Feb 5 02:40:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqn_62508/02_2026/9kqn_62508.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqn_62508/02_2026/9kqn_62508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kqn_62508/02_2026/9kqn_62508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqn_62508/02_2026/9kqn_62508.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqn_62508/02_2026/9kqn_62508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqn_62508/02_2026/9kqn_62508.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.059 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 5 5.49 5 S 76 5.16 5 C 9039 2.51 5 N 2442 2.21 5 O 2730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14292 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5141 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 15, 'TRANS': 616} Chain breaks: 1 Chain: "B" Number of atoms: 5150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5150 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 15, 'TRANS': 617} Chain breaks: 1 Chain: "C" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1821 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 11, 'TRANS': 222} Chain breaks: 1 Chain: "E" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2126 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 4, 'TRANS': 248} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.31, per 1000 atoms: 0.23 Number of scatterers: 14292 At special positions: 0 Unit cell: (122.628, 129.585, 133.934, 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 76 16.00 P 5 15.00 O 2730 8.00 N 2442 7.00 C 9039 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: 1.44 Conformation dependent library (CDL) restraints added in 519.2 milliseconds 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 10 sheets defined 51.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 66 removed outlier: 3.660A pdb=" N THR A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 4.118A pdb=" N SER A 72 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 192 through 198 removed outlier: 5.199A pdb=" N GLU A 196 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.579A pdb=" N TYR A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 406 through 428 removed outlier: 3.532A pdb=" N LYS A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 452 removed outlier: 6.716A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 removed outlier: 4.106A pdb=" N GLU A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 removed outlier: 3.868A pdb=" N TYR A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 554 through 579 removed outlier: 5.504A pdb=" N ASN A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 640 through 653 Processing helix chain 'A' and resid 656 through 674 Processing helix chain 'A' and resid 680 through 696 removed outlier: 4.311A pdb=" N HIS A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.878A pdb=" N PHE B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 66 removed outlier: 3.683A pdb=" N THR B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.910A pdb=" N SER B 72 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 113 through 122 removed outlier: 3.527A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.535A pdb=" N TYR B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 199 through 210 removed outlier: 3.552A pdb=" N ILE B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 406 through 428 Processing helix chain 'B' and resid 430 through 452 removed outlier: 6.717A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 461 removed outlier: 3.989A pdb=" N GLU B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 483 removed outlier: 3.868A pdb=" N TYR B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 504 Processing helix chain 'B' and resid 508 through 515 Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 554 through 579 removed outlier: 5.490A pdb=" N ASN B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 621 through 628 Processing helix chain 'B' and resid 640 through 653 Processing helix chain 'B' and resid 656 through 674 Processing helix chain 'B' and resid 680 through 697 removed outlier: 4.311A pdb=" N HIS B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 332 Processing helix chain 'C' and resid 335 through 357 Processing helix chain 'C' and resid 433 through 447 removed outlier: 3.506A pdb=" N TYR C 444 " --> pdb=" O GLY C 440 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 499 through 512 Processing helix chain 'C' and resid 519 through 523 removed outlier: 4.448A pdb=" N LEU C 522 " --> pdb=" O LEU C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 removed outlier: 3.729A pdb=" N LEU C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.520A pdb=" N LYS C 553 " --> pdb=" O CYS C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 580 Processing helix chain 'E' and resid 4 through 9 removed outlier: 4.020A pdb=" N HIS E 9 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 74 removed outlier: 3.556A pdb=" N ARG E 55 " --> pdb=" O ASP E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 112 removed outlier: 3.545A pdb=" N LEU E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 119 Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.836A pdb=" N ARG E 166 " --> pdb=" O PHE E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 176 Processing helix chain 'E' and resid 178 through 182 removed outlier: 3.514A pdb=" N LEU E 181 " --> pdb=" O ASN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 198 removed outlier: 3.858A pdb=" N ALA E 187 " --> pdb=" O CYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 225 removed outlier: 4.175A pdb=" N MET E 206 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLN E 212 " --> pdb=" O GLN E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 239 removed outlier: 3.512A pdb=" N CYS E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 251 through 273 removed outlier: 3.814A pdb=" N GLU E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.642A pdb=" N GLU A 18 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 90 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 78 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE B 221 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 80 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU B 223 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 220 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 222 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.535A pdb=" N GLN A 23 " --> pdb=" O ILE B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 289 removed outlier: 3.602A pdb=" N VAL A 222 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 78 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE A 221 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 80 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 147 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 18 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 332 removed outlier: 3.750A pdb=" N ALA A 325 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 362 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 363 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 470 through 475 removed outlier: 7.377A pdb=" N GLU A 473 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR A 467 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR A 466 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE A 491 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 588 removed outlier: 4.121A pdb=" N LYS A 585 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 368 through 372 removed outlier: 7.084A pdb=" N LEU B 363 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 325 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE E 124 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLU B 332 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP E 122 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 466 through 467 removed outlier: 4.487A pdb=" N TYR B 466 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE B 491 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 585 through 588 removed outlier: 6.527A pdb=" N LYS B 585 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE B 636 " --> pdb=" O LYS B 585 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.819A pdb=" N CYS C 323 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 373 " --> pdb=" O CYS C 377 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2043 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: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2684 1.32 - 1.44: 3458 1.44 - 1.56: 8263 1.56 - 1.69: 7 1.69 - 1.81: 122 Bond restraints: 14534 Sorted by residual: bond pdb=" CA TYR C 321 " pdb=" C TYR C 321 " ideal model delta sigma weight residual 1.525 1.454 0.071 1.12e-02 7.97e+03 4.06e+01 bond pdb=" CA THR C 538 " pdb=" C THR C 538 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.37e-02 5.33e+03 3.28e+01 bond pdb=" CA HIS C 360 " pdb=" C HIS C 360 " ideal model delta sigma weight residual 1.525 1.453 0.071 1.25e-02 6.40e+03 3.27e+01 bond pdb=" CA ARG C 326 " pdb=" C ARG C 326 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.35e-02 5.49e+03 3.08e+01 bond pdb=" CA ASP C 351 " pdb=" C ASP C 351 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.26e-02 6.30e+03 2.89e+01 ... (remaining 14529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 18316 2.37 - 4.74: 998 4.74 - 7.11: 176 7.11 - 9.49: 49 9.49 - 11.86: 15 Bond angle restraints: 19554 Sorted by residual: angle pdb=" N ILE A 131 " pdb=" CA ILE A 131 " pdb=" C ILE A 131 " ideal model delta sigma weight residual 110.30 120.65 -10.35 9.70e-01 1.06e+00 1.14e+02 angle pdb=" N THR A 36 " pdb=" CA THR A 36 " pdb=" C THR A 36 " ideal model delta sigma weight residual 111.36 122.05 -10.69 1.09e+00 8.42e-01 9.62e+01 angle pdb=" N TYR C 444 " pdb=" CA TYR C 444 " pdb=" C TYR C 444 " ideal model delta sigma weight residual 111.71 100.66 11.05 1.15e+00 7.56e-01 9.23e+01 angle pdb=" N GLY A 137 " pdb=" CA GLY A 137 " pdb=" C GLY A 137 " ideal model delta sigma weight residual 112.73 122.56 -9.83 1.20e+00 6.94e-01 6.72e+01 angle pdb=" N GLU A 75 " pdb=" CA GLU A 75 " pdb=" C GLU A 75 " ideal model delta sigma weight residual 111.07 119.54 -8.47 1.07e+00 8.73e-01 6.26e+01 ... (remaining 19549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.66: 8206 29.66 - 59.32: 668 59.32 - 88.98: 86 88.98 - 118.64: 3 118.64 - 148.30: 2 Dihedral angle restraints: 8965 sinusoidal: 3812 harmonic: 5153 Sorted by residual: dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 151.70 148.30 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 159.49 140.50 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 38.83 -98.83 1 2.00e+01 2.50e-03 2.77e+01 ... (remaining 8962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1886 0.107 - 0.215: 211 0.215 - 0.322: 61 0.322 - 0.429: 8 0.429 - 0.536: 1 Chirality restraints: 2167 Sorted by residual: chirality pdb=" CA ARG B 367 " pdb=" N ARG B 367 " pdb=" C ARG B 367 " pdb=" CB ARG B 367 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" CA LEU C 325 " pdb=" N LEU C 325 " pdb=" C LEU C 325 " pdb=" CB LEU C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA GLN C 491 " pdb=" N GLN C 491 " pdb=" C GLN C 491 " pdb=" CB GLN C 491 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 2164 not shown) Planarity restraints: 2491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 537 " -0.024 2.00e-02 2.50e+03 5.11e-02 2.62e+01 pdb=" C ALA C 537 " 0.088 2.00e-02 2.50e+03 pdb=" O ALA C 537 " -0.035 2.00e-02 2.50e+03 pdb=" N THR C 538 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 454 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C TYR C 454 " 0.066 2.00e-02 2.50e+03 pdb=" O TYR C 454 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY C 455 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 578 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.79e+00 pdb=" C ILE A 578 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE A 578 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 579 " 0.017 2.00e-02 2.50e+03 ... (remaining 2488 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1688 2.72 - 3.26: 15379 3.26 - 3.81: 23968 3.81 - 4.35: 29345 4.35 - 4.90: 46955 Nonbonded interactions: 117335 Sorted by model distance: nonbonded pdb=" O LEU A 463 " pdb=" NH1 ARG A 464 " model vdw 2.174 3.120 nonbonded pdb=" O LEU B 463 " pdb=" NH1 ARG B 464 " model vdw 2.175 3.120 nonbonded pdb=" OD1 ASN A 433 " pdb=" NZ LYS A 436 " model vdw 2.202 3.120 nonbonded pdb=" OD1 ASN B 433 " pdb=" NZ LYS B 436 " model vdw 2.202 3.120 nonbonded pdb=" O GLU A 380 " pdb=" ND2 ASN A 383 " model vdw 2.204 3.120 ... (remaining 117330 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' selection = (chain 'B' and (resid 15 through 227 or resid 280 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.750 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.011 0.107 14534 Z= 0.688 Angle : 1.280 11.858 19554 Z= 0.838 Chirality : 0.080 0.536 2167 Planarity : 0.005 0.051 2491 Dihedral : 20.376 148.299 5617 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 12.86 % Allowed : 25.40 % Favored : 61.74 % 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: -2.33 (0.18), residues: 1733 helix: -1.26 (0.17), residues: 813 sheet: -1.01 (0.33), residues: 238 loop : -1.93 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 262 TYR 0.028 0.002 TYR E 189 PHE 0.032 0.002 PHE E 162 TRP 0.027 0.003 TRP A 162 HIS 0.006 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.01102 (14534) covalent geometry : angle 1.28017 (19554) hydrogen bonds : bond 0.19352 ( 726) hydrogen bonds : angle 8.07210 ( 2043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 215 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8953 (t0) cc_final: 0.8170 (t0) REVERT: A 42 GLU cc_start: 0.9264 (pt0) cc_final: 0.8938 (pt0) REVERT: A 98 MET cc_start: 0.9220 (mtm) cc_final: 0.8936 (mtp) REVERT: A 128 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9066 (pp) REVERT: A 153 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7828 (tptp) REVERT: A 287 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8685 (mp10) REVERT: A 358 LYS cc_start: 0.8902 (mttt) cc_final: 0.8669 (mtmm) REVERT: A 371 MET cc_start: 0.8456 (ttp) cc_final: 0.8223 (ptm) REVERT: A 402 MET cc_start: 0.8661 (ptm) cc_final: 0.8460 (ptp) REVERT: A 421 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8518 (mp) REVERT: A 610 MET cc_start: 0.9046 (ttp) cc_final: 0.8626 (tpt) REVERT: A 614 MET cc_start: 0.9211 (mmm) cc_final: 0.8974 (mmt) REVERT: A 621 ASP cc_start: 0.9097 (m-30) cc_final: 0.8753 (t0) REVERT: B 77 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8114 (p-80) REVERT: B 119 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8918 (tmm) REVERT: B 157 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8949 (t0) REVERT: B 163 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: B 180 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7919 (ppp) REVERT: B 284 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7770 (m-10) REVERT: B 317 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8884 (p) REVERT: B 378 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9074 (pp) REVERT: B 473 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8609 (tm-30) REVERT: B 474 MET cc_start: 0.9377 (mtm) cc_final: 0.9086 (mtm) REVERT: B 498 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8641 (p) REVERT: B 547 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: B 621 ASP cc_start: 0.8259 (m-30) cc_final: 0.7859 (t0) REVERT: B 624 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7600 (t) REVERT: B 658 SER cc_start: 0.9630 (OUTLIER) cc_final: 0.9428 (p) REVERT: B 678 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8655 (pp) REVERT: C 319 LYS cc_start: 0.8396 (mmmm) cc_final: 0.7880 (mmmm) REVERT: C 525 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8509 (p0) REVERT: C 530 TRP cc_start: 0.6188 (t-100) cc_final: 0.5907 (t-100) REVERT: C 539 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7314 (pp) REVERT: C 547 LYS cc_start: 0.6261 (OUTLIER) cc_final: 0.5936 (mttp) REVERT: E 18 GLU cc_start: 0.8854 (mm-30) cc_final: 0.7707 (mm-30) REVERT: E 45 LYS cc_start: 0.9034 (tttp) cc_final: 0.8731 (tmmm) REVERT: E 102 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7988 (mp) REVERT: E 112 MET cc_start: 0.8380 (mmt) cc_final: 0.7957 (mmm) REVERT: E 158 GLN cc_start: 0.4917 (pp30) cc_final: 0.4698 (pp30) REVERT: E 162 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5924 (p90) REVERT: E 186 THR cc_start: 0.1162 (OUTLIER) cc_final: 0.0806 (t) REVERT: E 222 LEU cc_start: 0.5248 (tp) cc_final: 0.5034 (pp) outliers start: 202 outliers final: 44 residues processed: 385 average time/residue: 0.5887 time to fit residues: 249.1396 Evaluate side-chains 195 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 127 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 549 CYS Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 405 GLN A 450 HIS A 684 HIS A 686 ASN B 35 ASN B 77 HIS B 133 GLN B 189 HIS B 212 GLN B 488 GLN B 531 GLN B 622 ASN B 684 HIS B 686 ASN C 505 ASN C 542 ASN E 85 GLN E 172 GLN E 178 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.100363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.073314 restraints weight = 45511.118| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 4.57 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 14534 Z= 0.165 Angle : 0.712 10.446 19554 Z= 0.374 Chirality : 0.043 0.212 2167 Planarity : 0.005 0.066 2491 Dihedral : 10.611 128.172 2042 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.24 % Allowed : 30.74 % Favored : 63.02 % 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: -0.90 (0.19), residues: 1733 helix: 0.11 (0.18), residues: 826 sheet: -0.40 (0.34), residues: 236 loop : -1.47 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 226 TYR 0.027 0.002 TYR E 189 PHE 0.018 0.002 PHE E 162 TRP 0.021 0.002 TRP A 162 HIS 0.010 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00358 (14534) covalent geometry : angle 0.71156 (19554) hydrogen bonds : bond 0.05418 ( 726) hydrogen bonds : angle 5.46394 ( 2043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 157 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8913 (t0) cc_final: 0.8151 (t0) REVERT: A 42 GLU cc_start: 0.9328 (pt0) cc_final: 0.9095 (pt0) REVERT: A 45 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8811 (tm) REVERT: A 180 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8471 (ppp) REVERT: A 287 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8478 (mp10) REVERT: A 371 MET cc_start: 0.8414 (ttp) cc_final: 0.8184 (ptm) REVERT: A 610 MET cc_start: 0.9113 (ttp) cc_final: 0.8534 (tpt) REVERT: A 613 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9100 (tp) REVERT: A 614 MET cc_start: 0.9221 (mmm) cc_final: 0.8860 (mmm) REVERT: A 621 ASP cc_start: 0.9118 (m-30) cc_final: 0.8758 (t0) REVERT: B 40 ASN cc_start: 0.8912 (t0) cc_final: 0.8515 (t0) REVERT: B 157 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8960 (t0) REVERT: B 163 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: B 180 MET cc_start: 0.8167 (ptm) cc_final: 0.7966 (ppp) REVERT: B 201 ARG cc_start: 0.8972 (tmm-80) cc_final: 0.8575 (ttp80) REVERT: B 317 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8829 (p) REVERT: B 621 ASP cc_start: 0.8399 (m-30) cc_final: 0.7927 (t0) REVERT: B 625 MET cc_start: 0.8032 (mmt) cc_final: 0.7795 (mmt) REVERT: C 319 LYS cc_start: 0.8438 (mmmm) cc_final: 0.8138 (mmmm) REVERT: C 496 LYS cc_start: 0.9200 (mppt) cc_final: 0.8930 (mmmm) REVERT: C 553 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8386 (ttpp) REVERT: E 11 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: E 15 ASP cc_start: 0.8391 (p0) cc_final: 0.7352 (p0) REVERT: E 18 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8102 (mm-30) REVERT: E 44 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8471 (tm-30) REVERT: E 45 LYS cc_start: 0.9294 (tttp) cc_final: 0.8896 (tmmm) REVERT: E 59 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.5961 (ttp80) REVERT: E 132 LYS cc_start: 0.8189 (tttt) cc_final: 0.7692 (tptt) REVERT: E 211 HIS cc_start: 0.1142 (OUTLIER) cc_final: 0.0606 (p-80) REVERT: E 222 LEU cc_start: 0.4849 (tp) cc_final: 0.4618 (pp) REVERT: E 250 GLU cc_start: -0.0212 (OUTLIER) cc_final: -0.1023 (pt0) outliers start: 98 outliers final: 33 residues processed: 237 average time/residue: 0.5698 time to fit residues: 149.7875 Evaluate side-chains 176 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 250 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 104 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 404 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN E 85 GLN E 178 ASN ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.090171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065459 restraints weight = 46398.332| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 4.76 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14534 Z= 0.195 Angle : 0.655 8.351 19554 Z= 0.343 Chirality : 0.042 0.155 2167 Planarity : 0.004 0.072 2491 Dihedral : 8.278 107.808 1953 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.98 % Allowed : 30.74 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1733 helix: 0.52 (0.18), residues: 829 sheet: -0.09 (0.34), residues: 235 loop : -1.29 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 106 TYR 0.021 0.002 TYR E 174 PHE 0.024 0.002 PHE E 234 TRP 0.017 0.002 TRP C 530 HIS 0.010 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00433 (14534) covalent geometry : angle 0.65512 (19554) hydrogen bonds : bond 0.04943 ( 726) hydrogen bonds : angle 5.00976 ( 2043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 131 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8871 (t0) cc_final: 0.8038 (t0) REVERT: A 42 GLU cc_start: 0.9308 (pt0) cc_final: 0.8980 (pt0) REVERT: A 180 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8768 (ppp) REVERT: A 287 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8493 (mp10) REVERT: A 321 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8683 (mt-10) REVERT: A 350 ASP cc_start: 0.9260 (p0) cc_final: 0.8994 (p0) REVERT: A 371 MET cc_start: 0.8493 (ttp) cc_final: 0.8220 (ptm) REVERT: A 521 MET cc_start: 0.9287 (mtt) cc_final: 0.8739 (mtp) REVERT: A 610 MET cc_start: 0.9177 (ttp) cc_final: 0.8649 (tpt) REVERT: A 621 ASP cc_start: 0.9302 (m-30) cc_final: 0.8824 (t0) REVERT: B 30 MET cc_start: 0.9135 (tpp) cc_final: 0.8866 (mmm) REVERT: B 98 MET cc_start: 0.8756 (mtp) cc_final: 0.8204 (mtt) REVERT: B 180 MET cc_start: 0.8141 (ptm) cc_final: 0.7844 (ppp) REVERT: B 201 ARG cc_start: 0.9040 (tmm-80) cc_final: 0.8830 (tmm-80) REVERT: B 317 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8787 (p) REVERT: B 614 MET cc_start: 0.8366 (tpp) cc_final: 0.7983 (tmm) REVERT: B 621 ASP cc_start: 0.8478 (m-30) cc_final: 0.7957 (t0) REVERT: B 625 MET cc_start: 0.8050 (mmt) cc_final: 0.7257 (mmt) REVERT: B 678 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8532 (pp) REVERT: C 319 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8015 (mmmm) REVERT: C 496 LYS cc_start: 0.9204 (mppt) cc_final: 0.8897 (mmmm) REVERT: C 553 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8543 (ttpp) REVERT: C 561 ASN cc_start: 0.8916 (p0) cc_final: 0.8517 (p0) REVERT: E 9 HIS cc_start: 0.6545 (m-70) cc_final: 0.6324 (m-70) REVERT: E 18 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8456 (mm-30) REVERT: E 44 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8637 (tm-30) REVERT: E 45 LYS cc_start: 0.9251 (tttp) cc_final: 0.8779 (tmmm) REVERT: E 56 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: E 59 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.5821 (ttp80) REVERT: E 102 LEU cc_start: 0.8064 (tt) cc_final: 0.7757 (mp) REVERT: E 132 LYS cc_start: 0.8274 (tttt) cc_final: 0.7777 (tptt) REVERT: E 175 LEU cc_start: 0.7542 (tp) cc_final: 0.7332 (tp) REVERT: E 211 HIS cc_start: 0.1709 (OUTLIER) cc_final: 0.1271 (p-80) REVERT: E 214 ILE cc_start: 0.5414 (OUTLIER) cc_final: 0.5203 (mp) outliers start: 94 outliers final: 33 residues processed: 207 average time/residue: 0.5841 time to fit residues: 134.0481 Evaluate side-chains 162 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 23 optimal weight: 0.0040 chunk 42 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 HIS ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.089172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064462 restraints weight = 46511.480| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 5.17 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14534 Z= 0.199 Angle : 0.644 8.675 19554 Z= 0.334 Chirality : 0.041 0.165 2167 Planarity : 0.004 0.063 2491 Dihedral : 7.282 91.749 1939 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.73 % Allowed : 31.13 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1733 helix: 0.70 (0.18), residues: 834 sheet: -0.02 (0.34), residues: 244 loop : -1.16 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 201 TYR 0.030 0.002 TYR E 174 PHE 0.019 0.001 PHE E 252 TRP 0.022 0.002 TRP C 512 HIS 0.019 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00445 (14534) covalent geometry : angle 0.64418 (19554) hydrogen bonds : bond 0.04671 ( 726) hydrogen bonds : angle 4.81753 ( 2043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 134 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8834 (t0) cc_final: 0.8040 (t0) REVERT: A 42 GLU cc_start: 0.9298 (pt0) cc_final: 0.8957 (pt0) REVERT: A 321 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8813 (mt-10) REVERT: A 350 ASP cc_start: 0.9288 (p0) cc_final: 0.9040 (p0) REVERT: A 484 MET cc_start: 0.8621 (mpp) cc_final: 0.8397 (mpp) REVERT: A 610 MET cc_start: 0.9200 (ttp) cc_final: 0.8740 (tpt) REVERT: A 613 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9159 (tp) REVERT: A 621 ASP cc_start: 0.9286 (m-30) cc_final: 0.8814 (t0) REVERT: A 691 MET cc_start: 0.9525 (mmm) cc_final: 0.9081 (mmm) REVERT: B 30 MET cc_start: 0.9146 (tpp) cc_final: 0.8906 (mmm) REVERT: B 201 ARG cc_start: 0.9105 (tmm-80) cc_final: 0.8852 (tmm-80) REVERT: B 317 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8786 (p) REVERT: B 614 MET cc_start: 0.8281 (tpp) cc_final: 0.7871 (tmm) REVERT: B 621 ASP cc_start: 0.8465 (m-30) cc_final: 0.8045 (t0) REVERT: B 647 ARG cc_start: 0.9423 (OUTLIER) cc_final: 0.8927 (ptm-80) REVERT: B 678 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8426 (pp) REVERT: C 318 MET cc_start: 0.8778 (ptp) cc_final: 0.8409 (ptt) REVERT: C 319 LYS cc_start: 0.8238 (mmmm) cc_final: 0.7945 (mmmm) REVERT: C 496 LYS cc_start: 0.9172 (mppt) cc_final: 0.8813 (mmmm) REVERT: C 553 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8423 (ttpp) REVERT: C 561 ASN cc_start: 0.9016 (p0) cc_final: 0.8662 (p0) REVERT: E 11 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: E 18 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8406 (mm-30) REVERT: E 44 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8539 (tm-30) REVERT: E 45 LYS cc_start: 0.9272 (tttp) cc_final: 0.8875 (tmmm) REVERT: E 56 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: E 59 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.5808 (ttp80) REVERT: E 132 LYS cc_start: 0.8338 (tttt) cc_final: 0.7845 (tptt) REVERT: E 211 HIS cc_start: 0.1603 (OUTLIER) cc_final: 0.1047 (p-80) REVERT: E 222 LEU cc_start: 0.7787 (pp) cc_final: 0.7288 (tm) REVERT: E 225 SER cc_start: 0.6461 (t) cc_final: 0.6024 (m) outliers start: 90 outliers final: 29 residues processed: 210 average time/residue: 0.5681 time to fit residues: 132.8818 Evaluate side-chains 157 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 89 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 HIS E 180 HIS ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.092509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.066363 restraints weight = 45862.928| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.57 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14534 Z= 0.245 Angle : 0.679 9.367 19554 Z= 0.350 Chirality : 0.042 0.210 2167 Planarity : 0.004 0.058 2491 Dihedral : 6.894 73.142 1935 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.60 % Allowed : 31.25 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1733 helix: 0.69 (0.18), residues: 827 sheet: -0.05 (0.34), residues: 240 loop : -1.11 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 106 TYR 0.018 0.002 TYR A 434 PHE 0.029 0.002 PHE E 238 TRP 0.029 0.002 TRP C 512 HIS 0.018 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00550 (14534) covalent geometry : angle 0.67851 (19554) hydrogen bonds : bond 0.04753 ( 726) hydrogen bonds : angle 4.83585 ( 2043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 126 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8868 (t0) cc_final: 0.8091 (t0) REVERT: A 42 GLU cc_start: 0.9279 (pt0) cc_final: 0.8911 (pt0) REVERT: A 119 MET cc_start: 0.9275 (tpp) cc_final: 0.9073 (mmm) REVERT: A 335 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 484 MET cc_start: 0.8764 (mpp) cc_final: 0.8288 (mpt) REVERT: A 522 ILE cc_start: 0.9495 (pt) cc_final: 0.9233 (pp) REVERT: A 610 MET cc_start: 0.9210 (ttp) cc_final: 0.8690 (tpt) REVERT: A 621 ASP cc_start: 0.9288 (m-30) cc_final: 0.8798 (t0) REVERT: A 691 MET cc_start: 0.9527 (mmm) cc_final: 0.9141 (mmm) REVERT: B 30 MET cc_start: 0.9185 (tpp) cc_final: 0.8947 (mmm) REVERT: B 163 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8455 (tm-30) REVERT: B 201 ARG cc_start: 0.9116 (tmm-80) cc_final: 0.8889 (tmm-80) REVERT: B 317 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8768 (p) REVERT: B 372 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8867 (p0) REVERT: B 614 MET cc_start: 0.8417 (tpp) cc_final: 0.7762 (tmm) REVERT: B 621 ASP cc_start: 0.8491 (m-30) cc_final: 0.8096 (t0) REVERT: B 625 MET cc_start: 0.8039 (mmt) cc_final: 0.6711 (mmt) REVERT: B 678 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8517 (pp) REVERT: C 319 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7947 (mmmm) REVERT: C 466 TYR cc_start: 0.6925 (p90) cc_final: 0.6635 (p90) REVERT: C 496 LYS cc_start: 0.9239 (mppt) cc_final: 0.8894 (mtmm) REVERT: C 553 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8490 (ttpp) REVERT: C 561 ASN cc_start: 0.9142 (p0) cc_final: 0.8864 (p0) REVERT: E 11 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: E 18 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8466 (mm-30) REVERT: E 44 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8441 (tm-30) REVERT: E 45 LYS cc_start: 0.9279 (tttp) cc_final: 0.8916 (tmmm) REVERT: E 102 LEU cc_start: 0.8189 (tt) cc_final: 0.7823 (mp) REVERT: E 132 LYS cc_start: 0.8170 (tttt) cc_final: 0.7746 (tptt) outliers start: 88 outliers final: 36 residues processed: 200 average time/residue: 0.5157 time to fit residues: 115.8269 Evaluate side-chains 159 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 126 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN E 172 GLN E 180 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.095629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.069413 restraints weight = 44973.154| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.59 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14534 Z= 0.125 Angle : 0.639 11.594 19554 Z= 0.325 Chirality : 0.041 0.272 2167 Planarity : 0.004 0.068 2491 Dihedral : 6.461 63.311 1934 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.88 % Allowed : 33.29 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.20), residues: 1733 helix: 0.77 (0.18), residues: 837 sheet: 0.04 (0.33), residues: 242 loop : -0.94 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 264 TYR 0.015 0.001 TYR A 434 PHE 0.021 0.001 PHE E 234 TRP 0.032 0.002 TRP C 512 HIS 0.022 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00274 (14534) covalent geometry : angle 0.63908 (19554) hydrogen bonds : bond 0.04127 ( 726) hydrogen bonds : angle 4.66656 ( 2043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 131 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8948 (tpp) REVERT: A 40 ASN cc_start: 0.8766 (t0) cc_final: 0.7990 (t0) REVERT: A 42 GLU cc_start: 0.9232 (pt0) cc_final: 0.8870 (pt0) REVERT: A 474 MET cc_start: 0.9079 (mtt) cc_final: 0.8829 (mtp) REVERT: A 484 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8278 (mpp) REVERT: A 610 MET cc_start: 0.9116 (ttp) cc_final: 0.8648 (tpt) REVERT: A 613 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9231 (tp) REVERT: A 621 ASP cc_start: 0.9235 (m-30) cc_final: 0.8747 (t0) REVERT: A 691 MET cc_start: 0.9537 (mmm) cc_final: 0.9144 (mmm) REVERT: B 30 MET cc_start: 0.9157 (tpp) cc_final: 0.8932 (mmm) REVERT: B 163 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: B 317 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8700 (p) REVERT: B 614 MET cc_start: 0.8310 (tpp) cc_final: 0.7635 (tmm) REVERT: B 621 ASP cc_start: 0.8486 (m-30) cc_final: 0.8091 (t0) REVERT: B 625 MET cc_start: 0.8062 (mmt) cc_final: 0.7124 (mmt) REVERT: B 678 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8465 (pp) REVERT: C 318 MET cc_start: 0.8762 (ptp) cc_final: 0.8417 (ptp) REVERT: C 351 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8870 (t0) REVERT: C 496 LYS cc_start: 0.9258 (mppt) cc_final: 0.8899 (mmmm) REVERT: C 512 TRP cc_start: 0.7823 (m-90) cc_final: 0.7369 (m-90) REVERT: C 553 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8400 (ttpp) REVERT: C 561 ASN cc_start: 0.9134 (p0) cc_final: 0.8833 (p0) REVERT: E 9 HIS cc_start: 0.6827 (m-70) cc_final: 0.6603 (m170) REVERT: E 44 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8512 (tm-30) REVERT: E 45 LYS cc_start: 0.9287 (tttp) cc_final: 0.8858 (tmmm) REVERT: E 102 LEU cc_start: 0.8131 (tt) cc_final: 0.7837 (mp) REVERT: E 132 LYS cc_start: 0.8104 (tttt) cc_final: 0.7589 (tptt) REVERT: E 211 HIS cc_start: 0.1251 (OUTLIER) cc_final: 0.0962 (p-80) REVERT: E 222 LEU cc_start: 0.7541 (pp) cc_final: 0.7171 (tp) outliers start: 61 outliers final: 24 residues processed: 184 average time/residue: 0.5274 time to fit residues: 108.8222 Evaluate side-chains 152 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 169 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 HIS ** E 212 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 = 0.3719 r_free = 0.3719 target = 0.094707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068193 restraints weight = 45030.942| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.64 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14534 Z= 0.179 Angle : 0.673 11.471 19554 Z= 0.339 Chirality : 0.041 0.186 2167 Planarity : 0.004 0.064 2491 Dihedral : 6.275 61.358 1930 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.26 % Allowed : 33.29 % Favored : 62.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1733 helix: 0.76 (0.18), residues: 838 sheet: 0.07 (0.33), residues: 249 loop : -1.01 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 201 TYR 0.016 0.001 TYR A 434 PHE 0.024 0.001 PHE E 234 TRP 0.035 0.002 TRP C 530 HIS 0.020 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00407 (14534) covalent geometry : angle 0.67299 (19554) hydrogen bonds : bond 0.04225 ( 726) hydrogen bonds : angle 4.62382 ( 2043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 128 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8792 (t0) cc_final: 0.8107 (t0) REVERT: A 42 GLU cc_start: 0.9246 (pt0) cc_final: 0.8873 (pt0) REVERT: A 474 MET cc_start: 0.9109 (mtt) cc_final: 0.8855 (mtp) REVERT: A 484 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8298 (mpp) REVERT: A 610 MET cc_start: 0.9120 (ttp) cc_final: 0.8731 (tpp) REVERT: A 613 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9178 (tp) REVERT: A 621 ASP cc_start: 0.9237 (m-30) cc_final: 0.8750 (t0) REVERT: A 691 MET cc_start: 0.9558 (mmm) cc_final: 0.9189 (mmm) REVERT: B 30 MET cc_start: 0.9176 (tpp) cc_final: 0.8943 (mmm) REVERT: B 163 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8456 (tm-30) REVERT: B 317 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8715 (p) REVERT: B 371 MET cc_start: 0.9077 (ptm) cc_final: 0.8586 (ppp) REVERT: B 614 MET cc_start: 0.8324 (tpp) cc_final: 0.7560 (tmm) REVERT: B 621 ASP cc_start: 0.8576 (m-30) cc_final: 0.8103 (t0) REVERT: B 625 MET cc_start: 0.8090 (mmt) cc_final: 0.7137 (mmt) REVERT: B 678 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8419 (pp) REVERT: C 466 TYR cc_start: 0.6096 (p90) cc_final: 0.5880 (p90) REVERT: C 496 LYS cc_start: 0.9258 (mppt) cc_final: 0.8897 (mmmm) REVERT: C 512 TRP cc_start: 0.7967 (m-90) cc_final: 0.7650 (m-90) REVERT: C 561 ASN cc_start: 0.9181 (p0) cc_final: 0.8905 (p0) REVERT: E 9 HIS cc_start: 0.6859 (m-70) cc_final: 0.6617 (m170) REVERT: E 11 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: E 44 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8442 (tm-30) REVERT: E 45 LYS cc_start: 0.9321 (tttp) cc_final: 0.8992 (tmmm) REVERT: E 132 LYS cc_start: 0.8124 (tttt) cc_final: 0.7654 (tptt) REVERT: E 222 LEU cc_start: 0.7470 (pp) cc_final: 0.7045 (tp) outliers start: 67 outliers final: 28 residues processed: 182 average time/residue: 0.4282 time to fit residues: 88.1163 Evaluate side-chains 151 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 547 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 5 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 160 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 HIS ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.096126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.069945 restraints weight = 44546.497| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.58 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14534 Z= 0.124 Angle : 0.662 12.257 19554 Z= 0.331 Chirality : 0.041 0.182 2167 Planarity : 0.004 0.057 2491 Dihedral : 6.107 61.860 1930 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.44 % Allowed : 34.63 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1733 helix: 0.79 (0.18), residues: 840 sheet: 0.25 (0.33), residues: 245 loop : -1.02 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 106 TYR 0.036 0.001 TYR E 174 PHE 0.022 0.001 PHE B 349 TRP 0.041 0.002 TRP C 530 HIS 0.022 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00277 (14534) covalent geometry : angle 0.66240 (19554) hydrogen bonds : bond 0.03843 ( 726) hydrogen bonds : angle 4.49366 ( 2043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8808 (t0) cc_final: 0.7950 (t0) REVERT: A 42 GLU cc_start: 0.9188 (pt0) cc_final: 0.8777 (pt0) REVERT: A 196 GLU cc_start: 0.9555 (pt0) cc_final: 0.9257 (pp20) REVERT: A 484 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8232 (mpp) REVERT: A 610 MET cc_start: 0.9041 (ttp) cc_final: 0.8621 (tpt) REVERT: A 613 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9149 (tp) REVERT: A 621 ASP cc_start: 0.9198 (m-30) cc_final: 0.8693 (OUTLIER) REVERT: A 691 MET cc_start: 0.9541 (mmm) cc_final: 0.9190 (mmm) REVERT: B 119 MET cc_start: 0.9432 (tpp) cc_final: 0.9204 (mmm) REVERT: B 163 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: B 317 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 614 MET cc_start: 0.8377 (tpp) cc_final: 0.7600 (tmm) REVERT: B 621 ASP cc_start: 0.8478 (m-30) cc_final: 0.8083 (OUTLIER) REVERT: B 678 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8377 (pp) REVERT: C 496 LYS cc_start: 0.9268 (mppt) cc_final: 0.8932 (mmmm) REVERT: C 561 ASN cc_start: 0.9159 (p0) cc_final: 0.8860 (p0) REVERT: C 575 CYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6744 (m) REVERT: E 9 HIS cc_start: 0.6916 (m-70) cc_final: 0.6668 (m-70) REVERT: E 11 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: E 42 GLN cc_start: 0.9220 (tp-100) cc_final: 0.8879 (tp-100) REVERT: E 44 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8369 (tm-30) REVERT: E 45 LYS cc_start: 0.9306 (tttp) cc_final: 0.8979 (tmmm) REVERT: E 105 MET cc_start: 0.9020 (mmm) cc_final: 0.8670 (mmm) REVERT: E 106 ARG cc_start: 0.9161 (mmm160) cc_final: 0.8799 (tpp80) REVERT: E 108 LYS cc_start: 0.9557 (mtmm) cc_final: 0.9257 (mttp) REVERT: E 132 LYS cc_start: 0.8059 (tttt) cc_final: 0.7606 (tptp) REVERT: E 222 LEU cc_start: 0.7406 (pp) cc_final: 0.6928 (mt) outliers start: 54 outliers final: 25 residues processed: 176 average time/residue: 0.5300 time to fit residues: 104.0397 Evaluate side-chains 149 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 142 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 HIS ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.093646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.067589 restraints weight = 45710.368| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.61 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14534 Z= 0.187 Angle : 0.707 11.655 19554 Z= 0.354 Chirality : 0.042 0.220 2167 Planarity : 0.004 0.077 2491 Dihedral : 6.073 60.553 1923 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.61 % Allowed : 35.46 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.20), residues: 1733 helix: 0.75 (0.18), residues: 841 sheet: 0.25 (0.34), residues: 247 loop : -1.02 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 201 TYR 0.016 0.001 TYR A 434 PHE 0.022 0.002 PHE B 349 TRP 0.048 0.002 TRP C 530 HIS 0.021 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00426 (14534) covalent geometry : angle 0.70725 (19554) hydrogen bonds : bond 0.04188 ( 726) hydrogen bonds : angle 4.59132 ( 2043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8849 (t0) cc_final: 0.8007 (t0) REVERT: A 42 GLU cc_start: 0.9202 (pt0) cc_final: 0.8830 (pt0) REVERT: A 196 GLU cc_start: 0.9546 (pt0) cc_final: 0.9235 (pp20) REVERT: A 484 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8309 (mpp) REVERT: A 610 MET cc_start: 0.9124 (ttp) cc_final: 0.8763 (tpp) REVERT: A 613 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9186 (tp) REVERT: A 621 ASP cc_start: 0.9204 (m-30) cc_final: 0.8689 (t0) REVERT: A 691 MET cc_start: 0.9566 (mmm) cc_final: 0.9237 (mmm) REVERT: B 163 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: B 317 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8716 (p) REVERT: B 473 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: B 614 MET cc_start: 0.8477 (tpp) cc_final: 0.7632 (tmm) REVERT: B 621 ASP cc_start: 0.8487 (m-30) cc_final: 0.8055 (OUTLIER) REVERT: B 678 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8380 (pp) REVERT: C 496 LYS cc_start: 0.9275 (mppt) cc_final: 0.8912 (mmmm) REVERT: C 512 TRP cc_start: 0.8021 (m-90) cc_final: 0.7700 (m-90) REVERT: C 561 ASN cc_start: 0.9215 (p0) cc_final: 0.8931 (p0) REVERT: E 9 HIS cc_start: 0.6946 (m-70) cc_final: 0.6718 (m170) REVERT: E 11 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8035 (pt0) REVERT: E 44 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8291 (tm-30) REVERT: E 45 LYS cc_start: 0.9362 (tttp) cc_final: 0.9000 (tmmm) REVERT: E 132 LYS cc_start: 0.8072 (tttt) cc_final: 0.7625 (tptp) REVERT: E 222 LEU cc_start: 0.7401 (pp) cc_final: 0.6911 (mt) outliers start: 41 outliers final: 23 residues processed: 157 average time/residue: 0.5796 time to fit residues: 101.1169 Evaluate side-chains 149 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 155 TYR Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 53 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 532 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 HIS ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.094111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.068238 restraints weight = 44725.937| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.53 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14534 Z= 0.137 Angle : 0.701 12.027 19554 Z= 0.348 Chirality : 0.041 0.205 2167 Planarity : 0.004 0.064 2491 Dihedral : 5.986 61.322 1923 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.36 % Allowed : 35.77 % Favored : 61.87 % 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 (0.20), residues: 1733 helix: 0.76 (0.18), residues: 841 sheet: 0.29 (0.33), residues: 249 loop : -1.02 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 106 TYR 0.014 0.001 TYR A 434 PHE 0.023 0.001 PHE B 349 TRP 0.054 0.002 TRP C 530 HIS 0.021 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00313 (14534) covalent geometry : angle 0.70069 (19554) hydrogen bonds : bond 0.03877 ( 726) hydrogen bonds : angle 4.52781 ( 2043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8808 (t0) cc_final: 0.7974 (t0) REVERT: A 42 GLU cc_start: 0.9164 (pt0) cc_final: 0.8776 (pt0) REVERT: A 98 MET cc_start: 0.8793 (mmt) cc_final: 0.8319 (mmt) REVERT: A 196 GLU cc_start: 0.9553 (pt0) cc_final: 0.9237 (pp20) REVERT: A 610 MET cc_start: 0.9066 (ttp) cc_final: 0.8663 (tpt) REVERT: A 613 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9171 (tp) REVERT: A 621 ASP cc_start: 0.9168 (m-30) cc_final: 0.8676 (t0) REVERT: A 691 MET cc_start: 0.9547 (mmm) cc_final: 0.9198 (mmm) REVERT: B 163 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: B 201 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8548 (tmm160) REVERT: B 317 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 614 MET cc_start: 0.8486 (tpp) cc_final: 0.7596 (tmm) REVERT: B 621 ASP cc_start: 0.8463 (m-30) cc_final: 0.8058 (t0) REVERT: B 678 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8346 (pp) REVERT: C 496 LYS cc_start: 0.9280 (mppt) cc_final: 0.8944 (mmmm) REVERT: C 512 TRP cc_start: 0.7971 (m-90) cc_final: 0.7740 (m-90) REVERT: C 561 ASN cc_start: 0.9208 (p0) cc_final: 0.8898 (p0) REVERT: C 575 CYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6817 (m) REVERT: E 9 HIS cc_start: 0.6980 (m-70) cc_final: 0.6749 (m-70) REVERT: E 11 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: E 42 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8802 (tp-100) REVERT: E 44 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8317 (tm-30) REVERT: E 45 LYS cc_start: 0.9344 (tttp) cc_final: 0.8961 (tmmm) REVERT: E 106 ARG cc_start: 0.9113 (mmm160) cc_final: 0.8847 (tpm-80) REVERT: E 132 LYS cc_start: 0.8038 (tttt) cc_final: 0.7599 (tptp) REVERT: E 214 ILE cc_start: 0.5274 (OUTLIER) cc_final: 0.4908 (mp) REVERT: E 222 LEU cc_start: 0.7420 (pp) cc_final: 0.6952 (mt) outliers start: 37 outliers final: 22 residues processed: 159 average time/residue: 0.5684 time to fit residues: 100.1327 Evaluate side-chains 152 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 155 TYR Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 134 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.092762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.066566 restraints weight = 45606.575| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.61 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14534 Z= 0.234 Angle : 0.754 14.109 19554 Z= 0.376 Chirality : 0.043 0.213 2167 Planarity : 0.004 0.067 2491 Dihedral : 6.133 61.282 1923 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.16 % Allowed : 36.16 % Favored : 61.68 % 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: -0.06 (0.20), residues: 1733 helix: 0.71 (0.18), residues: 838 sheet: 0.24 (0.34), residues: 247 loop : -1.07 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 106 TYR 0.017 0.001 TYR C 444 PHE 0.024 0.002 PHE E 238 TRP 0.055 0.003 TRP C 530 HIS 0.009 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00533 (14534) covalent geometry : angle 0.75410 (19554) hydrogen bonds : bond 0.04348 ( 726) hydrogen bonds : angle 4.69341 ( 2043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4784.65 seconds wall clock time: 82 minutes 46.58 seconds (4966.58 seconds total)