Starting phenix.real_space_refine on Sat Aug 8 14:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oke_70561/08_2026/9oke_70561.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oke_70561/08_2026/9oke_70561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oke_70561/08_2026/9oke_70561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oke_70561/08_2026/9oke_70561.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oke_70561/08_2026/9oke_70561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oke_70561/08_2026/9oke_70561.map" } resolution = 3.24 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= -0.000 sd= 0.010 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 S 66 5.16 5 C 8924 2.51 5 N 2387 2.21 5 O 2601 1.98 5 H 14040 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28018 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2295 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "K" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1906 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "I" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5752 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 337} Chain: "M" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 2614 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 157} Chain: "L" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3880 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 4 Chain: "N" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5155 Classifications: {'peptide': 324} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain breaks: 1 Chain: "O" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2804 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain breaks: 2 Chain: "P" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3404 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain breaks: 1 Chain: "T" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 208 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 4.29, per 1000 atoms: 0.15 Number of scatterers: 28018 At special positions: 0 Unit cell: (98.884, 118.158, 177.656, 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 66 16.00 O 2601 8.00 N 2387 7.00 C 8924 6.00 H 14040 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 28 " distance=2.04 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: 2.61 Conformation dependent library (CDL) restraints added in 932.2 milliseconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 9 sheets defined 61.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'H' and resid 34 through 61 removed outlier: 4.041A pdb=" N LYS H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 63 through 68 Processing helix chain 'H' and resid 73 through 108 removed outlier: 4.054A pdb=" N LYS H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 114 through 169 Processing helix chain 'K' and resid 3 through 34 removed outlier: 3.794A pdb=" N GLU K 32 " --> pdb=" O CYS K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 62 Processing helix chain 'K' and resid 71 through 123 Processing helix chain 'I' and resid 309 through 313 Processing helix chain 'I' and resid 315 through 334 removed outlier: 3.695A pdb=" N HIS I 328 " --> pdb=" O HIS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 360 Processing helix chain 'I' and resid 363 through 374 Processing helix chain 'I' and resid 375 through 377 No H-bonds generated for 'chain 'I' and resid 375 through 377' Processing helix chain 'I' and resid 382 through 391 removed outlier: 3.700A pdb=" N GLU I 391 " --> pdb=" O LEU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 413 removed outlier: 4.216A pdb=" N LEU I 401 " --> pdb=" O SER I 397 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY I 402 " --> pdb=" O PRO I 398 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR I 403 " --> pdb=" O ASP I 399 " (cutoff:3.500A) Proline residue: I 407 - end of helix Processing helix chain 'I' and resid 416 through 438 Processing helix chain 'I' and resid 444 through 448 removed outlier: 3.827A pdb=" N ILE I 448 " --> pdb=" O PHE I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 477 removed outlier: 4.009A pdb=" N TYR I 455 " --> pdb=" O PRO I 451 " (cutoff:3.500A) Proline residue: I 460 - end of helix removed outlier: 3.738A pdb=" N TYR I 476 " --> pdb=" O LYS I 472 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN I 477 " --> pdb=" O ALA I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 501 Processing helix chain 'I' and resid 510 through 520 removed outlier: 3.789A pdb=" N LEU I 514 " --> pdb=" O GLY I 510 " (cutoff:3.500A) Proline residue: I 517 - end of helix Processing helix chain 'I' and resid 522 through 547 removed outlier: 3.895A pdb=" N ILE I 526 " --> pdb=" O SER I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 573 removed outlier: 3.592A pdb=" N LEU I 570 " --> pdb=" O ASP I 566 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR I 571 " --> pdb=" O LEU I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 582 Processing helix chain 'I' and resid 584 through 588 Processing helix chain 'I' and resid 589 through 600 Processing helix chain 'I' and resid 602 through 607 removed outlier: 3.646A pdb=" N LYS I 606 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU I 607 " --> pdb=" O PRO I 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 602 through 607' Processing helix chain 'I' and resid 612 through 624 removed outlier: 3.609A pdb=" N ALA I 617 " --> pdb=" O VAL I 613 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR I 618 " --> pdb=" O ALA I 614 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL I 621 " --> pdb=" O ALA I 617 " (cutoff:3.500A) Processing helix chain 'I' and resid 629 through 632 Processing helix chain 'I' and resid 633 through 645 Processing helix chain 'I' and resid 645 through 656 Processing helix chain 'I' and resid 656 through 661 removed outlier: 3.589A pdb=" N ARG I 660 " --> pdb=" O VAL I 656 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET I 661 " --> pdb=" O PRO I 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 656 through 661' Processing helix chain 'M' and resid 31 through 49 Processing helix chain 'M' and resid 63 through 73 removed outlier: 3.928A pdb=" N VAL M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 102 removed outlier: 3.691A pdb=" N TRP M 95 " --> pdb=" O PHE M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 108 Processing helix chain 'M' and resid 121 through 125 removed outlier: 3.879A pdb=" N MET M 125 " --> pdb=" O VAL M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 139 Processing helix chain 'M' and resid 150 through 170 Processing helix chain 'L' and resid 50 through 67 Processing helix chain 'L' and resid 142 through 158 Processing helix chain 'L' and resid 167 through 182 Processing helix chain 'L' and resid 211 through 221 Processing helix chain 'L' and resid 227 through 248 Processing helix chain 'L' and resid 276 through 291 removed outlier: 3.654A pdb=" N VAL L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE L 284 " --> pdb=" O VAL L 280 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE L 290 " --> pdb=" O VAL L 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 17 removed outlier: 3.598A pdb=" N LYS N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 25 Processing helix chain 'N' and resid 25 through 30 Processing helix chain 'N' and resid 33 through 43 Processing helix chain 'N' and resid 49 through 65 removed outlier: 5.131A pdb=" N LYS N 63 " --> pdb=" O ARG N 59 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER N 64 " --> pdb=" O HIS N 60 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU N 65 " --> pdb=" O ILE N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 83 removed outlier: 4.052A pdb=" N ILE N 73 " --> pdb=" O GLU N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 120 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 173 through 185 removed outlier: 3.502A pdb=" N GLY N 185 " --> pdb=" O VAL N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 207 Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.543A pdb=" N ASP N 242 " --> pdb=" O ASN N 238 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA N 243 " --> pdb=" O ARG N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 299 Processing helix chain 'N' and resid 306 through 311 removed outlier: 4.020A pdb=" N PHE N 309 " --> pdb=" O SER N 306 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE N 311 " --> pdb=" O PHE N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 327 Processing helix chain 'O' and resid 79 through 93 Processing helix chain 'O' and resid 128 through 131 Processing helix chain 'O' and resid 144 through 150 removed outlier: 3.739A pdb=" N VAL O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 186 Processing helix chain 'O' and resid 260 through 269 Processing helix chain 'P' and resid 68 through 87 Processing helix chain 'P' and resid 157 through 166 removed outlier: 4.041A pdb=" N LYS P 166 " --> pdb=" O THR P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 172 Proline residue: P 170 - end of helix No H-bonds generated for 'chain 'P' and resid 167 through 172' Processing helix chain 'P' and resid 174 through 204 Processing helix chain 'P' and resid 253 through 267 removed outlier: 3.567A pdb=" N GLU P 262 " --> pdb=" O ALA P 258 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA P 263 " --> pdb=" O LYS P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 291 removed outlier: 3.910A pdb=" N VAL P 291 " --> pdb=" O VAL P 287 " (cutoff:3.500A) Processing helix chain 'T' and resid 813 through 836 Processing sheet with id=AA1, first strand: chain 'M' and resid 54 through 60 removed outlier: 6.661A pdb=" N LEU M 23 " --> pdb=" O VAL M 56 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU M 58 " --> pdb=" O LEU M 23 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA M 25 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N SER M 60 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL M 27 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE M 82 " --> pdb=" O THR M 24 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE M 26 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA M 84 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU M 28 " --> pdb=" O ALA M 84 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP M 142 " --> pdb=" O VAL M 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 34 through 37 removed outlier: 4.964A pdb=" N GLY L 34 " --> pdb=" O MET L 274 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET L 274 " --> pdb=" O GLY L 34 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY L 271 " --> pdb=" O LYS L 267 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL L 193 " --> pdb=" O SER L 257 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE L 259 " --> pdb=" O THR L 191 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR L 191 " --> pdb=" O ILE L 259 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER L 208 " --> pdb=" O LYS N 281 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP L 210 " --> pdb=" O ASN N 279 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN N 279 " --> pdb=" O ASP L 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 77 through 84 removed outlier: 6.163A pdb=" N SER L 103 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL L 113 " --> pdb=" O SER L 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 127 through 135 removed outlier: 6.462A pdb=" N LEU N 139 " --> pdb=" O ALA N 158 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA N 158 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE N 141 " --> pdb=" O TYR N 156 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR N 156 " --> pdb=" O ILE N 141 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL N 143 " --> pdb=" O THR N 154 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR N 154 " --> pdb=" O VAL N 143 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU N 145 " --> pdb=" O GLY N 152 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU N 194 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN N 93 " --> pdb=" O ALA N 192 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA N 192 " --> pdb=" O ASN N 93 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N SER N 95 " --> pdb=" O GLU N 190 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU N 190 " --> pdb=" O SER N 95 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN N 97 " --> pdb=" O LYS N 188 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LYS N 188 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 228 through 229 removed outlier: 3.533A pdb=" N ILE N 228 " --> pdb=" O ASN N 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 94 through 100 removed outlier: 5.966A pdb=" N MET O 94 " --> pdb=" O HIS O 110 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N HIS O 110 " --> pdb=" O MET O 94 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL O 96 " --> pdb=" O VAL O 108 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL O 108 " --> pdb=" O VAL O 96 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER O 98 " --> pdb=" O CYS O 106 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU O 126 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL O 134 " --> pdb=" O GLU O 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 190 through 192 Processing sheet with id=AA8, first strand: chain 'P' and resid 92 through 97 removed outlier: 4.317A pdb=" N TYR P 135 " --> pdb=" O LYS P 150 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS P 150 " --> pdb=" O TYR P 135 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N HIS P 137 " --> pdb=" O TYR P 148 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR P 148 " --> pdb=" O HIS P 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 207 through 211 884 hydrogen bonds defined for protein. 2556 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: 7.56 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 14015 1.04 - 1.24: 1917 1.24 - 1.44: 3943 1.44 - 1.64: 8271 1.64 - 1.85: 107 Bond restraints: 28253 Sorted by residual: bond pdb=" N MET N 1 " pdb=" H2 MET N 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N MET N 1 " pdb=" H3 MET N 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N MET N 1 " pdb=" CA MET N 1 " ideal model delta sigma weight residual 1.491 1.457 0.034 2.10e-02 2.27e+03 2.60e+00 bond pdb=" N MET N 1 " pdb=" H1 MET N 1 " ideal model delta sigma weight residual 0.890 0.861 0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" N LEU N 27 " pdb=" CA LEU N 27 " ideal model delta sigma weight residual 1.462 1.452 0.011 7.70e-03 1.69e+04 1.89e+00 ... (remaining 28248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.36: 51111 7.36 - 14.71: 1 14.71 - 22.07: 1 22.07 - 29.42: 0 29.42 - 36.78: 6 Bond angle restraints: 51119 Sorted by residual: angle pdb=" C ASN N 235 " pdb=" CA ASN N 235 " pdb=" HA ASN N 235 " ideal model delta sigma weight residual 109.00 72.22 36.78 3.00e+00 1.11e-01 1.50e+02 angle pdb=" CB THR N 25 " pdb=" CA THR N 25 " pdb=" HA THR N 25 " ideal model delta sigma weight residual 109.00 73.85 35.15 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N ASN N 235 " pdb=" CA ASN N 235 " pdb=" HA ASN N 235 " ideal model delta sigma weight residual 110.00 75.21 34.79 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C THR N 25 " pdb=" CA THR N 25 " pdb=" HA THR N 25 " ideal model delta sigma weight residual 109.00 75.01 33.99 3.00e+00 1.11e-01 1.28e+02 angle pdb=" N THR N 25 " pdb=" CA THR N 25 " pdb=" HA THR N 25 " ideal model delta sigma weight residual 110.00 76.92 33.08 3.00e+00 1.11e-01 1.22e+02 ... (remaining 51114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 12073 17.51 - 35.02: 859 35.02 - 52.53: 210 52.53 - 70.05: 61 70.05 - 87.56: 28 Dihedral angle restraints: 13231 sinusoidal: 7305 harmonic: 5926 Sorted by residual: dihedral pdb=" CB CYS K 24 " pdb=" SG CYS K 24 " pdb=" SG CYS K 28 " pdb=" CB CYS K 28 " ideal model delta sinusoidal sigma weight residual -86.00 -127.02 41.02 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" C THR N 25 " pdb=" N THR N 25 " pdb=" CA THR N 25 " pdb=" CB THR N 25 " ideal model delta harmonic sigma weight residual -122.00 -133.60 11.60 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" CA VAL N 41 " pdb=" C VAL N 41 " pdb=" N ARG N 42 " pdb=" CA ARG N 42 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 13228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2135 0.085 - 0.170: 121 0.170 - 0.255: 0 0.255 - 0.340: 0 0.340 - 0.425: 2 Chirality restraints: 2258 Sorted by residual: chirality pdb=" CA THR N 25 " pdb=" N THR N 25 " pdb=" C THR N 25 " pdb=" CB THR N 25 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA ASN N 235 " pdb=" N ASN N 235 " pdb=" C ASN N 235 " pdb=" CB ASN N 235 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ILE N 141 " pdb=" N ILE N 141 " pdb=" C ILE N 141 " pdb=" CB ILE N 141 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 2255 not shown) Planarity restraints: 4067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU K 25 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C LEU K 25 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU K 25 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN K 26 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU O 139 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO O 140 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO O 140 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO O 140 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 111 " -0.135 9.50e-02 1.11e+02 4.58e-02 3.42e+00 pdb=" NE ARG M 111 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG M 111 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG M 111 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG M 111 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG M 111 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG M 111 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARG M 111 " 0.008 2.00e-02 2.50e+03 pdb="HH22 ARG M 111 " -0.007 2.00e-02 2.50e+03 ... (remaining 4064 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1164 2.18 - 2.78: 56323 2.78 - 3.39: 78096 3.39 - 3.99: 98001 3.99 - 4.60: 154604 Nonbonded interactions: 388188 Sorted by model distance: nonbonded pdb=" OE1 GLN I 591 " pdb=" H GLN I 591 " model vdw 1.571 2.450 nonbonded pdb=" H ASN N 235 " pdb=" HA ASN N 235 " model vdw 1.592 1.816 nonbonded pdb=" OE1 GLU L 278 " pdb=" H GLU L 278 " model vdw 1.597 2.450 nonbonded pdb=" H THR N 25 " pdb=" HA THR N 25 " model vdw 1.603 1.816 nonbonded pdb=" HA THR N 25 " pdb=" HB THR N 25 " model vdw 1.612 1.952 ... (remaining 388183 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.690 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: 0.180 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 27.900 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14214 Z= 0.133 Angle : 0.517 6.373 19220 Z= 0.293 Chirality : 0.040 0.425 2258 Planarity : 0.004 0.059 2419 Dihedral : 13.603 87.556 5357 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.03 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.21), residues: 1714 helix: 2.38 (0.18), residues: 930 sheet: 0.39 (0.33), residues: 252 loop : -0.36 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 111 TYR 0.011 0.001 TYR I 563 PHE 0.008 0.001 PHE N 269 TRP 0.009 0.001 TRP L 36 HIS 0.006 0.001 HIS I 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (14213) covalent geometry : angle 0.51639 / 0.29 (19218) SS BOND : bond 0.01188 / 0.63 ( 1) SS BOND : angle 2.72565 / 1.55 ( 2) hydrogen bonds : bond 0.13664 / 8.90 ( 884) hydrogen bonds : angle 5.57711 / 4.14 ( 2556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 322 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.666 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 351 ARG cc_start: 0.7386 (mpt-90) cc_final: 0.7058 (ttt-90) REVERT: I 380 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7978 (mtm180) REVERT: I 442 ARG cc_start: 0.7902 (ptm160) cc_final: 0.7654 (ptm160) REVERT: I 468 GLU cc_start: 0.7846 (tp30) cc_final: 0.7358 (tt0) REVERT: I 476 TYR cc_start: 0.7479 (p90) cc_final: 0.7202 (p90) REVERT: I 579 ARG cc_start: 0.7809 (ptt-90) cc_final: 0.7435 (ptm-80) REVERT: I 595 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7799 (mtpt) REVERT: M 52 ARG cc_start: 0.7431 (tpp80) cc_final: 0.7213 (tpp80) REVERT: M 68 LYS cc_start: 0.5306 (tmmt) cc_final: 0.4600 (mmtt) REVERT: M 111 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.7722 (mpp80) REVERT: L 60 LYS cc_start: 0.7425 (mttt) cc_final: 0.7103 (mtpp) REVERT: L 237 GLN cc_start: 0.8002 (tp40) cc_final: 0.7798 (tt0) REVERT: L 255 ASP cc_start: 0.8347 (p0) cc_final: 0.8028 (p0) REVERT: N 215 GLN cc_start: 0.7332 (tm-30) cc_final: 0.6206 (mm-40) REVERT: N 266 LYS cc_start: 0.7125 (mttt) cc_final: 0.6706 (mmmt) REVERT: O 186 ASN cc_start: 0.8001 (t0) cc_final: 0.7513 (t0) REVERT: O 232 LYS cc_start: 0.8304 (tppt) cc_final: 0.8075 (tptp) REVERT: O 233 GLN cc_start: 0.7800 (pt0) cc_final: 0.7579 (pt0) REVERT: P 245 MET cc_start: 0.6284 (mpp) cc_final: 0.6071 (mtt) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2826 time to fit residues: 127.6792 Evaluate side-chains 211 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 152 HIS I 487 ASN I 598 HIS M 134 ASN N 232 ASN N 313 HIS P 89 GLN T 819 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.216518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.190153 restraints weight = 43882.007| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.04 r_work: 0.3822 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14214 Z= 0.140 Angle : 0.522 6.520 19220 Z= 0.281 Chirality : 0.040 0.418 2258 Planarity : 0.004 0.073 2419 Dihedral : 4.062 69.843 1881 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.92 % Favored : 96.97 % Rotamer: Outliers : 0.70 % Allowed : 5.11 % Favored : 94.19 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.21), residues: 1714 helix: 2.48 (0.17), residues: 945 sheet: 0.25 (0.33), residues: 263 loop : -0.46 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 124 TYR 0.022 0.001 TYR M 136 PHE 0.013 0.001 PHE L 209 TRP 0.007 0.001 TRP L 36 HIS 0.005 0.001 HIS I 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14213) covalent geometry : angle 0.52160 / 0.28 (19218) SS BOND : bond 0.01091 / 0.57 ( 1) SS BOND : angle 2.32304 / 1.33 ( 2) hydrogen bonds : bond 0.05001 / 3.33 ( 884) hydrogen bonds : angle 4.38515 / 3.22 ( 2556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 0.724 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: I 340 TYR cc_start: 0.7128 (m-80) cc_final: 0.6919 (m-80) REVERT: I 351 ARG cc_start: 0.7866 (mpt-90) cc_final: 0.7277 (ttt-90) REVERT: I 380 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8139 (mtm180) REVERT: I 476 TYR cc_start: 0.7180 (p90) cc_final: 0.6890 (p90) REVERT: M 21 ASN cc_start: 0.7891 (t0) cc_final: 0.7543 (t0) REVERT: M 23 LEU cc_start: 0.8352 (pp) cc_final: 0.7975 (mp) REVERT: M 68 LYS cc_start: 0.5529 (tmmt) cc_final: 0.4801 (mmtt) REVERT: L 237 GLN cc_start: 0.8313 (tp40) cc_final: 0.8111 (tt0) REVERT: N 215 GLN cc_start: 0.7333 (tm-30) cc_final: 0.6392 (mm110) REVERT: N 266 LYS cc_start: 0.7128 (mttt) cc_final: 0.6825 (mmtm) REVERT: O 186 ASN cc_start: 0.7787 (t0) cc_final: 0.7386 (t0) REVERT: O 228 ASP cc_start: 0.8441 (m-30) cc_final: 0.8240 (m-30) REVERT: O 230 ARG cc_start: 0.8552 (mpt180) cc_final: 0.8343 (mmt-90) REVERT: P 126 ASP cc_start: 0.6117 (t0) cc_final: 0.5895 (t70) outliers start: 11 outliers final: 8 residues processed: 217 average time/residue: 0.2594 time to fit residues: 80.9169 Evaluate side-chains 199 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 575 SER Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain N residue 137 ASP Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain P residue 235 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 153 ASN L 39 ASN N 195 HIS P 137 HIS ** T 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.210908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.174830 restraints weight = 43832.517| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.39 r_work: 0.3640 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14214 Z= 0.190 Angle : 0.547 5.333 19220 Z= 0.294 Chirality : 0.042 0.426 2258 Planarity : 0.004 0.080 2419 Dihedral : 4.327 80.916 1881 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.15 % Favored : 96.73 % Rotamer: Outliers : 0.64 % Allowed : 7.02 % Favored : 92.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1714 helix: 2.23 (0.17), residues: 950 sheet: -0.02 (0.33), residues: 264 loop : -0.78 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 111 TYR 0.025 0.002 TYR M 136 PHE 0.015 0.002 PHE N 308 TRP 0.008 0.001 TRP I 392 HIS 0.006 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (14213) covalent geometry : angle 0.54637 / 0.29 (19218) SS BOND : bond 0.00915 / 0.48 ( 1) SS BOND : angle 2.26784 / 1.31 ( 2) hydrogen bonds : bond 0.05033 / 3.36 ( 884) hydrogen bonds : angle 4.32745 / 3.18 ( 2556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.650 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: K 69 THR cc_start: 0.7678 (p) cc_final: 0.7444 (t) REVERT: K 106 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8014 (tt0) REVERT: K 107 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7380 (tm-30) REVERT: I 351 ARG cc_start: 0.8166 (mpt-90) cc_final: 0.7503 (ttt180) REVERT: I 380 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8124 (mtm-85) REVERT: I 579 ARG cc_start: 0.7999 (ptt-90) cc_final: 0.7619 (ptm-80) REVERT: I 618 TYR cc_start: 0.7146 (m-80) cc_final: 0.6919 (m-80) REVERT: I 653 LYS cc_start: 0.7706 (mmtt) cc_final: 0.6869 (ttpt) REVERT: M 23 LEU cc_start: 0.8813 (pp) cc_final: 0.8177 (mp) REVERT: M 68 LYS cc_start: 0.5769 (tmmt) cc_final: 0.4808 (mmtt) REVERT: L 82 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6514 (tm-30) REVERT: L 237 GLN cc_start: 0.8370 (tp40) cc_final: 0.8099 (tt0) REVERT: N 215 GLN cc_start: 0.7595 (tm-30) cc_final: 0.6550 (mm-40) REVERT: O 186 ASN cc_start: 0.8028 (t0) cc_final: 0.7568 (t0) REVERT: O 228 ASP cc_start: 0.8499 (m-30) cc_final: 0.8267 (m-30) outliers start: 10 outliers final: 10 residues processed: 212 average time/residue: 0.2585 time to fit residues: 78.8435 Evaluate side-chains 198 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 575 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain N residue 137 ASP Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain P residue 137 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 107 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 chunk 144 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 33 ASN I 598 HIS M 134 ASN O 84 ASN P 137 HIS ** T 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.209216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.167043 restraints weight = 43299.764| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.54 r_work: 0.3482 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14214 Z= 0.169 Angle : 0.525 7.969 19220 Z= 0.281 Chirality : 0.041 0.421 2258 Planarity : 0.004 0.059 2419 Dihedral : 4.250 76.821 1881 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Rotamer: Outliers : 0.89 % Allowed : 8.24 % Favored : 90.87 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.21), residues: 1714 helix: 2.30 (0.17), residues: 948 sheet: -0.16 (0.33), residues: 260 loop : -0.82 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 494 TYR 0.021 0.001 TYR I 476 PHE 0.013 0.001 PHE P 143 TRP 0.008 0.001 TRP I 392 HIS 0.005 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (14213) covalent geometry : angle 0.52422 / 0.28 (19218) SS BOND : bond 0.01018 / 0.54 ( 1) SS BOND : angle 2.21744 / 1.28 ( 2) hydrogen bonds : bond 0.04766 / 3.17 ( 884) hydrogen bonds : angle 4.19692 / 3.07 ( 2556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.730 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: K 69 THR cc_start: 0.7857 (p) cc_final: 0.7632 (t) REVERT: K 107 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7507 (tm-30) REVERT: I 351 ARG cc_start: 0.8116 (mpt-90) cc_final: 0.7474 (ttt180) REVERT: I 380 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8122 (mtm-85) REVERT: I 579 ARG cc_start: 0.8007 (ptt-90) cc_final: 0.7125 (ptm-80) REVERT: I 618 TYR cc_start: 0.7266 (m-80) cc_final: 0.6990 (m-80) REVERT: I 653 LYS cc_start: 0.7723 (mmtt) cc_final: 0.6927 (ttpt) REVERT: M 23 LEU cc_start: 0.8901 (pp) cc_final: 0.8181 (mp) REVERT: M 68 LYS cc_start: 0.5736 (tmmt) cc_final: 0.4730 (mmtt) REVERT: L 237 GLN cc_start: 0.8309 (tp40) cc_final: 0.8062 (tt0) REVERT: L 279 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7374 (mt) REVERT: N 215 GLN cc_start: 0.7595 (tm-30) cc_final: 0.6526 (mm110) REVERT: O 86 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7336 (tt0) REVERT: O 152 TYR cc_start: 0.8054 (m-80) cc_final: 0.7376 (m-80) REVERT: O 186 ASN cc_start: 0.8111 (t0) cc_final: 0.7604 (t0) REVERT: O 228 ASP cc_start: 0.8522 (m-30) cc_final: 0.8240 (m-30) outliers start: 14 outliers final: 12 residues processed: 200 average time/residue: 0.2551 time to fit residues: 74.5170 Evaluate side-chains 197 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 575 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 279 ILE Chi-restraints excluded: chain N residue 137 ASP Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 137 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 6 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 598 HIS L 39 ASN N 206 ASN ** T 813 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 = 0.4315 r_free = 0.4315 target = 0.210315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.172013 restraints weight = 43848.393| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.43 r_work: 0.3550 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14214 Z= 0.164 Angle : 0.508 6.204 19220 Z= 0.272 Chirality : 0.040 0.413 2258 Planarity : 0.004 0.057 2419 Dihedral : 4.224 78.146 1881 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.92 % Favored : 96.97 % Rotamer: Outliers : 0.89 % Allowed : 9.07 % Favored : 90.04 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.21), residues: 1714 helix: 2.36 (0.17), residues: 946 sheet: -0.20 (0.33), residues: 260 loop : -0.84 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 494 TYR 0.019 0.001 TYR I 476 PHE 0.013 0.001 PHE P 143 TRP 0.008 0.001 TRP I 392 HIS 0.007 0.001 HIS P 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (14213) covalent geometry : angle 0.50784 / 0.27 (19218) SS BOND : bond 0.01031 / 0.54 ( 1) SS BOND : angle 2.22143 / 1.28 ( 2) hydrogen bonds : bond 0.04688 / 3.13 ( 884) hydrogen bonds : angle 4.14278 / 3.02 ( 2556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.679 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: K 69 THR cc_start: 0.8005 (p) cc_final: 0.7784 (t) REVERT: K 106 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8024 (tt0) REVERT: K 107 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7224 (mt-10) REVERT: I 351 ARG cc_start: 0.8090 (mpt-90) cc_final: 0.7485 (ttt180) REVERT: I 380 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8161 (mtm-85) REVERT: I 579 ARG cc_start: 0.8023 (ptt-90) cc_final: 0.7162 (ptm-80) REVERT: I 618 TYR cc_start: 0.7422 (m-80) cc_final: 0.7132 (m-80) REVERT: M 23 LEU cc_start: 0.8964 (pp) cc_final: 0.8181 (mp) REVERT: M 68 LYS cc_start: 0.5783 (tmmt) cc_final: 0.4793 (mmtt) REVERT: L 237 GLN cc_start: 0.8326 (tp40) cc_final: 0.8120 (tt0) REVERT: L 279 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7467 (mt) REVERT: N 215 GLN cc_start: 0.7587 (tm-30) cc_final: 0.6539 (mm110) REVERT: O 186 ASN cc_start: 0.8054 (t0) cc_final: 0.7611 (t0) REVERT: O 228 ASP cc_start: 0.8518 (m-30) cc_final: 0.8201 (m-30) REVERT: O 230 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.8479 (mmt-90) outliers start: 14 outliers final: 13 residues processed: 197 average time/residue: 0.2492 time to fit residues: 71.9295 Evaluate side-chains 199 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 575 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 279 ILE Chi-restraints excluded: chain N residue 137 ASP Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain O residue 148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 89 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 0.0670 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 598 HIS N 206 ASN ** T 813 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 = 0.4306 r_free = 0.4306 target = 0.208880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167582 restraints weight = 43399.952| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.60 r_work: 0.3473 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14214 Z= 0.131 Angle : 0.488 5.345 19220 Z= 0.259 Chirality : 0.039 0.400 2258 Planarity : 0.003 0.056 2419 Dihedral : 4.110 74.020 1881 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Rotamer: Outliers : 1.02 % Allowed : 9.39 % Favored : 89.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.21), residues: 1714 helix: 2.58 (0.17), residues: 934 sheet: -0.15 (0.34), residues: 254 loop : -0.75 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 16 TYR 0.018 0.001 TYR M 136 PHE 0.010 0.001 PHE P 143 TRP 0.007 0.001 TRP I 636 HIS 0.004 0.001 HIS I 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (14213) covalent geometry : angle 0.48768 / 0.26 (19218) SS BOND : bond 0.01157 / 0.61 ( 1) SS BOND : angle 2.20501 / 1.27 ( 2) hydrogen bonds : bond 0.04347 / 2.90 ( 884) hydrogen bonds : angle 4.01012 / 2.92 ( 2556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.754 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: K 69 THR cc_start: 0.8067 (p) cc_final: 0.7827 (t) REVERT: K 106 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7997 (tt0) REVERT: K 107 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7211 (mt-10) REVERT: I 351 ARG cc_start: 0.8111 (mpt-90) cc_final: 0.7444 (ttt180) REVERT: I 380 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8126 (mtm-85) REVERT: I 579 ARG cc_start: 0.7983 (ptt-90) cc_final: 0.7104 (ptm-80) REVERT: I 618 TYR cc_start: 0.7435 (m-80) cc_final: 0.7166 (m-80) REVERT: I 653 LYS cc_start: 0.7731 (tptt) cc_final: 0.6865 (ttpt) REVERT: M 49 SER cc_start: 0.8499 (t) cc_final: 0.8230 (m) REVERT: M 68 LYS cc_start: 0.5874 (tmmt) cc_final: 0.4867 (mmtt) REVERT: L 237 GLN cc_start: 0.8308 (tp40) cc_final: 0.8086 (tt0) REVERT: L 279 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7458 (mp) REVERT: N 215 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6516 (mm110) REVERT: O 152 TYR cc_start: 0.7941 (m-80) cc_final: 0.7291 (m-80) REVERT: O 186 ASN cc_start: 0.8120 (t0) cc_final: 0.7671 (t0) outliers start: 16 outliers final: 15 residues processed: 200 average time/residue: 0.2763 time to fit residues: 80.1430 Evaluate side-chains 203 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 575 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 279 ILE Chi-restraints excluded: chain N residue 137 ASP Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 252 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 598 HIS L 39 ASN N 206 ASN ** T 813 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 = 0.4314 r_free = 0.4314 target = 0.208992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.170968 restraints weight = 43380.757| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.38 r_work: 0.3525 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14214 Z= 0.195 Angle : 0.531 5.463 19220 Z= 0.284 Chirality : 0.041 0.412 2258 Planarity : 0.004 0.055 2419 Dihedral : 4.309 83.292 1881 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.33 % Favored : 96.56 % Rotamer: Outliers : 1.34 % Allowed : 9.64 % Favored : 89.02 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.21), residues: 1714 helix: 2.38 (0.17), residues: 940 sheet: -0.29 (0.33), residues: 254 loop : -0.94 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 494 TYR 0.022 0.001 TYR I 476 PHE 0.016 0.001 PHE N 308 TRP 0.009 0.001 TRP I 392 HIS 0.004 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 (14213) covalent geometry : angle 0.53041 / 0.28 (19218) SS BOND : bond 0.00970 / 0.51 ( 1) SS BOND : angle 2.32721 / 1.35 ( 2) hydrogen bonds : bond 0.04844 / 3.22 ( 884) hydrogen bonds : angle 4.14031 / 3.01 ( 2556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 69 THR cc_start: 0.8182 (p) cc_final: 0.7973 (t) REVERT: K 106 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8022 (tt0) REVERT: K 107 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7353 (mt-10) REVERT: K 119 GLN cc_start: 0.7770 (tp-100) cc_final: 0.7120 (tp-100) REVERT: I 351 ARG cc_start: 0.8167 (mpt-90) cc_final: 0.7523 (ttt180) REVERT: I 380 ARG cc_start: 0.8707 (mmm-85) cc_final: 0.8192 (mtm-85) REVERT: I 579 ARG cc_start: 0.8062 (ptt-90) cc_final: 0.7356 (ptt180) REVERT: I 643 HIS cc_start: 0.7345 (m-70) cc_final: 0.7005 (m-70) REVERT: I 653 LYS cc_start: 0.7839 (tptt) cc_final: 0.6987 (ttpt) REVERT: M 49 SER cc_start: 0.8496 (t) cc_final: 0.8252 (m) REVERT: M 68 LYS cc_start: 0.5937 (tmmt) cc_final: 0.4909 (mmtt) REVERT: M 138 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6999 (mt-10) REVERT: L 82 GLU cc_start: 0.6697 (tm-30) cc_final: 0.5469 (tm-30) REVERT: L 237 GLN cc_start: 0.8260 (tp40) cc_final: 0.8059 (tt0) REVERT: L 279 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7593 (mp) REVERT: N 139 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7916 (tp) REVERT: N 215 GLN cc_start: 0.7614 (tm-30) cc_final: 0.6717 (mm-40) REVERT: N 266 LYS cc_start: 0.7246 (mttt) cc_final: 0.6747 (mmtm) REVERT: O 86 GLU cc_start: 0.7775 (tt0) cc_final: 0.7470 (tm-30) REVERT: O 186 ASN cc_start: 0.8124 (t0) cc_final: 0.7701 (t0) outliers start: 21 outliers final: 19 residues processed: 193 average time/residue: 0.2802 time to fit residues: 78.0979 Evaluate side-chains 196 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 575 SER Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 279 ILE Chi-restraints excluded: chain N residue 137 ASP Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 135 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 598 HIS N 206 ASN ** T 813 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 = 0.4337 r_free = 0.4337 target = 0.211556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174236 restraints weight = 43501.137| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.40 r_work: 0.3581 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14214 Z= 0.115 Angle : 0.483 5.040 19220 Z= 0.256 Chirality : 0.039 0.395 2258 Planarity : 0.003 0.058 2419 Dihedral : 4.113 73.750 1881 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Rotamer: Outliers : 1.15 % Allowed : 10.47 % Favored : 88.38 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.21), residues: 1714 helix: 2.63 (0.17), residues: 933 sheet: -0.26 (0.33), residues: 254 loop : -0.79 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 16 TYR 0.016 0.001 TYR M 136 PHE 0.010 0.001 PHE P 143 TRP 0.006 0.001 TRP I 392 HIS 0.003 0.001 HIS I 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (14213) covalent geometry : angle 0.48263 / 0.26 (19218) SS BOND : bond 0.01267 / 0.67 ( 1) SS BOND : angle 2.23820 / 1.29 ( 2) hydrogen bonds : bond 0.04228 / 2.81 ( 884) hydrogen bonds : angle 3.96118 / 2.89 ( 2556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.670 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: K 106 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8068 (tt0) REVERT: K 107 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7367 (mt-10) REVERT: K 122 MET cc_start: 0.7020 (mmm) cc_final: 0.6812 (mtp) REVERT: I 336 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: I 351 ARG cc_start: 0.8245 (mpt-90) cc_final: 0.7572 (ttt180) REVERT: I 380 ARG cc_start: 0.8630 (mmm-85) cc_final: 0.8175 (mtm-85) REVERT: I 579 ARG cc_start: 0.8028 (ptt-90) cc_final: 0.7192 (ptm-80) REVERT: I 643 HIS cc_start: 0.7349 (m-70) cc_final: 0.7008 (m-70) REVERT: I 653 LYS cc_start: 0.7908 (tptt) cc_final: 0.7021 (ttpt) REVERT: M 49 SER cc_start: 0.8427 (t) cc_final: 0.8211 (m) REVERT: M 68 LYS cc_start: 0.6049 (tmmt) cc_final: 0.5114 (mmtt) REVERT: M 138 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6917 (mt-10) REVERT: L 60 LYS cc_start: 0.7313 (mtpt) cc_final: 0.7093 (mttt) REVERT: L 279 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7586 (mp) REVERT: N 215 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6724 (mm-40) REVERT: O 86 GLU cc_start: 0.7799 (tt0) cc_final: 0.7588 (tm-30) REVERT: O 152 TYR cc_start: 0.7600 (m-80) cc_final: 0.7075 (m-80) REVERT: O 186 ASN cc_start: 0.8049 (t0) cc_final: 0.7660 (t0) outliers start: 18 outliers final: 15 residues processed: 199 average time/residue: 0.2710 time to fit residues: 77.6369 Evaluate side-chains 193 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 279 ILE Chi-restraints excluded: chain N residue 137 ASP Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 252 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 148 optimal weight: 0.0050 chunk 118 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 164 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 598 HIS L 39 ASN L 154 GLN N 206 ASN ** T 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.212160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175884 restraints weight = 43604.997| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.38 r_work: 0.3613 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14214 Z= 0.108 Angle : 0.472 5.263 19220 Z= 0.251 Chirality : 0.039 0.397 2258 Planarity : 0.003 0.060 2419 Dihedral : 4.015 71.408 1881 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % Rotamer: Outliers : 1.09 % Allowed : 10.66 % Favored : 88.25 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.21), residues: 1714 helix: 2.79 (0.17), residues: 935 sheet: -0.21 (0.34), residues: 254 loop : -0.72 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 263 TYR 0.016 0.001 TYR M 136 PHE 0.008 0.001 PHE I 373 TRP 0.005 0.001 TRP I 377 HIS 0.004 0.001 HIS P 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14213) covalent geometry : angle 0.47102 / 0.25 (19218) SS BOND : bond 0.01294 / 0.68 ( 1) SS BOND : angle 2.22730 / 1.28 ( 2) hydrogen bonds : bond 0.04014 / 2.67 ( 884) hydrogen bonds : angle 3.85603 / 2.82 ( 2556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.721 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: K 106 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7994 (tt0) REVERT: K 107 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7302 (mt-10) REVERT: K 119 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7081 (tp-100) REVERT: K 122 MET cc_start: 0.7100 (mmm) cc_final: 0.6763 (mtp) REVERT: I 351 ARG cc_start: 0.8166 (mpt-90) cc_final: 0.7501 (ttt180) REVERT: I 380 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8177 (mtm-85) REVERT: I 579 ARG cc_start: 0.7952 (ptt-90) cc_final: 0.7126 (ptm-80) REVERT: I 643 HIS cc_start: 0.7312 (m-70) cc_final: 0.6953 (m-70) REVERT: I 653 LYS cc_start: 0.7827 (tptt) cc_final: 0.6920 (ttpt) REVERT: M 68 LYS cc_start: 0.5970 (tmmt) cc_final: 0.5019 (mmtt) REVERT: M 138 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6900 (mt-10) REVERT: L 276 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7947 (t) REVERT: N 88 MET cc_start: 0.8739 (mmt) cc_final: 0.8492 (mmt) REVERT: N 215 GLN cc_start: 0.7467 (tm-30) cc_final: 0.6638 (mm110) REVERT: O 86 GLU cc_start: 0.7779 (tt0) cc_final: 0.7491 (tm-30) REVERT: O 186 ASN cc_start: 0.8060 (t0) cc_final: 0.7662 (t0) outliers start: 17 outliers final: 14 residues processed: 191 average time/residue: 0.2728 time to fit residues: 74.6207 Evaluate side-chains 189 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 279 ILE Chi-restraints excluded: chain N residue 137 ASP Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 252 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 155 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.207394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.169042 restraints weight = 43204.005| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.47 r_work: 0.3559 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14214 Z= 0.142 Angle : 0.492 5.107 19220 Z= 0.262 Chirality : 0.040 0.399 2258 Planarity : 0.004 0.059 2419 Dihedral : 4.153 79.398 1881 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.74 % Favored : 97.14 % Rotamer: Outliers : 1.15 % Allowed : 10.73 % Favored : 88.12 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.21), residues: 1714 helix: 2.66 (0.17), residues: 941 sheet: -0.30 (0.33), residues: 255 loop : -0.77 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 277 TYR 0.019 0.001 TYR M 136 PHE 0.012 0.001 PHE N 308 TRP 0.007 0.001 TRP I 392 HIS 0.004 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (14213) covalent geometry : angle 0.49120 / 0.26 (19218) SS BOND : bond 0.01150 / 0.61 ( 1) SS BOND : angle 2.25846 / 1.30 ( 2) hydrogen bonds : bond 0.04325 / 2.87 ( 884) hydrogen bonds : angle 3.90899 / 2.85 ( 2556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 46 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.777 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: K 106 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8063 (tt0) REVERT: K 107 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7384 (mt-10) REVERT: K 119 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7153 (tp-100) REVERT: I 336 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8428 (t0) REVERT: I 351 ARG cc_start: 0.8329 (mpt-90) cc_final: 0.7636 (ttt180) REVERT: I 380 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8129 (mtm-85) REVERT: I 579 ARG cc_start: 0.8102 (ptt-90) cc_final: 0.7200 (ptm-80) REVERT: I 643 HIS cc_start: 0.7374 (m-70) cc_final: 0.7030 (m-70) REVERT: I 653 LYS cc_start: 0.7961 (tptt) cc_final: 0.7039 (ttpt) REVERT: M 68 LYS cc_start: 0.6089 (tmmt) cc_final: 0.5183 (mmtt) REVERT: M 138 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7066 (mt-10) REVERT: L 157 PHE cc_start: 0.7364 (m-10) cc_final: 0.7054 (m-80) REVERT: L 276 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.8050 (t) REVERT: N 88 MET cc_start: 0.8783 (mmt) cc_final: 0.8556 (mmt) REVERT: N 139 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7661 (tp) REVERT: N 215 GLN cc_start: 0.7475 (tm-30) cc_final: 0.6715 (mm-40) REVERT: O 86 GLU cc_start: 0.7838 (tt0) cc_final: 0.7550 (tm-30) REVERT: O 186 ASN cc_start: 0.7978 (t0) cc_final: 0.7457 (m-40) outliers start: 18 outliers final: 15 residues processed: 186 average time/residue: 0.2789 time to fit residues: 74.6467 Evaluate side-chains 186 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 575 SER Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 279 ILE Chi-restraints excluded: chain N residue 137 ASP Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain P residue 127 LEU Chi-restraints excluded: chain P residue 252 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 39 ASN ** T 813 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 = 0.4308 r_free = 0.4308 target = 0.209356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173872 restraints weight = 43712.287| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.39 r_work: 0.3623 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14214 Z= 0.140 Angle : 0.489 5.328 19220 Z= 0.260 Chirality : 0.040 0.397 2258 Planarity : 0.004 0.059 2419 Dihedral : 4.114 77.010 1881 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.63 % Favored : 97.26 % Rotamer: Outliers : 1.34 % Allowed : 10.60 % Favored : 88.06 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.21), residues: 1714 helix: 2.70 (0.17), residues: 934 sheet: -0.33 (0.34), residues: 255 loop : -0.80 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 263 TYR 0.018 0.001 TYR M 136 PHE 0.011 0.001 PHE I 373 TRP 0.007 0.001 TRP I 392 HIS 0.004 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (14213) covalent geometry : angle 0.48822 / 0.26 (19218) SS BOND : bond 0.01194 / 0.63 ( 1) SS BOND : angle 2.31495 / 1.33 ( 2) hydrogen bonds : bond 0.04288 / 2.85 ( 884) hydrogen bonds : angle 3.90523 / 2.85 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6281.11 seconds wall clock time: 107 minutes 13.87 seconds (6433.87 seconds total)