Starting phenix.real_space_refine on Wed Mar 4 03:08:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm2_13510/03_2026/7pm2_13510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm2_13510/03_2026/7pm2_13510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pm2_13510/03_2026/7pm2_13510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm2_13510/03_2026/7pm2_13510.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pm2_13510/03_2026/7pm2_13510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm2_13510/03_2026/7pm2_13510.map" } resolution = 3.6 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= 0.001 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: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6475 2.51 5 N 1721 2.21 5 O 1893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10156 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6117 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 27, 'TRANS': 721} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.21, per 1000 atoms: 0.22 Number of scatterers: 10156 At special positions: 0 Unit cell: (104.5, 133.1, 148.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1893 8.00 N 1721 7.00 C 6475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 510.2 milliseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 56.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.202A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 116 through 120 removed outlier: 4.239A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.755A pdb=" N ASN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 4.501A pdb=" N MET A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.530A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.595A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.696A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.605A pdb=" N VAL A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.248A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 278 Proline residue: A 272 - end of helix removed outlier: 5.616A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 278 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.160A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.782A pdb=" N GLU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.565A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.652A pdb=" N ASP A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.765A pdb=" N MET A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.632A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.648A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.613A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.522A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.637A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 704 through 712 removed outlier: 4.098A pdb=" N SER A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.698A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.703A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 128 removed outlier: 3.881A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.627A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.520A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.627A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.696A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.260A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.531A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.439A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 347 removed outlier: 4.473A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 375 removed outlier: 3.922A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.506A pdb=" N LEU A 107 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE A 662 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 109 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.853A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.655A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.923A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 504 hydrogen bonds defined for protein. 1416 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: 1.72 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2792 1.33 - 1.47: 2913 1.47 - 1.60: 4562 1.60 - 1.73: 3 1.73 - 1.86: 102 Bond restraints: 10372 Sorted by residual: bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.86e+00 bond pdb=" O2 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" O1 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.565 1.509 0.056 2.00e-02 2.50e+03 7.89e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.79e+00 ... (remaining 10367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 13620 2.21 - 4.42: 340 4.42 - 6.63: 36 6.63 - 8.84: 5 8.84 - 11.05: 7 Bond angle restraints: 14008 Sorted by residual: angle pdb=" CA MET A 783 " pdb=" CB MET A 783 " pdb=" CG MET A 783 " ideal model delta sigma weight residual 114.10 104.80 9.30 2.00e+00 2.50e-01 2.16e+01 angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" C VAL A 427 " ideal model delta sigma weight residual 108.42 103.00 5.42 1.43e+00 4.89e-01 1.44e+01 angle pdb=" C1' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C3' ADP C 401 " ideal model delta sigma weight residual 111.00 99.95 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 128.90 118.29 10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C THR A 426 " pdb=" N VAL A 427 " pdb=" CA VAL A 427 " ideal model delta sigma weight residual 122.23 127.26 -5.03 1.44e+00 4.82e-01 1.22e+01 ... (remaining 14003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 6128 35.65 - 71.30: 103 71.30 - 106.94: 29 106.94 - 142.59: 6 142.59 - 178.24: 12 Dihedral angle restraints: 6278 sinusoidal: 2599 harmonic: 3679 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 169.96 130.04 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" CA LYS A 584 " pdb=" C LYS A 584 " pdb=" N LYS A 585 " pdb=" CA LYS A 585 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ILE C 289 " pdb=" C ILE C 289 " pdb=" N ARG C 290 " pdb=" CA ARG C 290 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 6275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1324 0.078 - 0.156: 188 0.156 - 0.234: 11 0.234 - 0.312: 2 0.312 - 0.390: 2 Chirality restraints: 1527 Sorted by residual: chirality pdb=" C10 9UE C 404 " pdb=" C18 9UE C 404 " pdb=" C9 9UE C 404 " pdb=" N2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C3 9UE C 404 " pdb=" O 9UE C 404 " pdb=" C2 9UE C 404 " pdb=" C35 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.21 2.57 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C1 9UE C 404 " pdb=" C 9UE C 404 " pdb=" C15 9UE C 404 " pdb=" C2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1524 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 701 " 0.160 9.50e-02 1.11e+02 9.19e-02 4.41e+01 pdb=" NE ARG A 701 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 701 " 0.109 2.00e-02 2.50e+03 pdb=" NH1 ARG A 701 " -0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG A 701 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " -0.135 9.50e-02 1.11e+02 7.88e-02 3.39e+01 pdb=" NE ARG A 710 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " -0.096 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " 0.140 9.50e-02 1.11e+02 7.50e-02 2.37e+01 pdb=" NE ARG A 92 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " 0.078 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " -0.021 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 108 2.65 - 3.21: 9680 3.21 - 3.77: 14842 3.77 - 4.34: 20984 4.34 - 4.90: 34216 Nonbonded interactions: 79830 Sorted by model distance: nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 403 " model vdw 2.085 2.170 nonbonded pdb=" OH TYR A 528 " pdb=" O ALA A 547 " model vdw 2.182 3.040 nonbonded pdb=" NH1 ARG A 213 " pdb=" O THR A 443 " model vdw 2.197 3.120 nonbonded pdb=" OG SER A 78 " pdb=" O ALA A 753 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.237 3.040 ... (remaining 79825 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10372 Z= 0.211 Angle : 0.859 11.049 14008 Z= 0.497 Chirality : 0.054 0.390 1527 Planarity : 0.008 0.093 1793 Dihedral : 18.701 178.239 3906 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.21), residues: 1238 helix: -1.72 (0.17), residues: 585 sheet: 0.38 (0.38), residues: 157 loop : -0.14 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.111 0.011 ARG A 701 TYR 0.036 0.006 TYR C 198 PHE 0.020 0.002 PHE A 673 TRP 0.030 0.003 TRP C 356 HIS 0.009 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00448 (10372) covalent geometry : angle 0.85887 (14008) hydrogen bonds : bond 0.16030 ( 502) hydrogen bonds : angle 7.82157 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8141 (m-80) cc_final: 0.7475 (m-10) REVERT: B 110 ARG cc_start: 0.8848 (mtt-85) cc_final: 0.8508 (mtt-85) REVERT: B 121 THR cc_start: 0.8417 (p) cc_final: 0.8175 (p) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1209 time to fit residues: 29.9339 Evaluate side-chains 94 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 123 optimal weight: 0.0040 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 136 ASN A 39 GLN A 264 GLN A 395 HIS ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN A 726 GLN C 12 ASN C 59 GLN C 353 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.084109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061611 restraints weight = 31052.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.063887 restraints weight = 15068.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065427 restraints weight = 9371.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066463 restraints weight = 6752.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067165 restraints weight = 5372.651| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10372 Z= 0.137 Angle : 0.637 7.553 14008 Z= 0.333 Chirality : 0.044 0.323 1527 Planarity : 0.004 0.036 1793 Dihedral : 18.036 168.311 1427 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.39 % Allowed : 5.91 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1238 helix: 0.64 (0.20), residues: 603 sheet: 0.51 (0.37), residues: 169 loop : 0.50 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 41 TYR 0.014 0.001 TYR A 711 PHE 0.018 0.002 PHE B 70 TRP 0.015 0.002 TRP A 414 HIS 0.009 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00299 (10372) covalent geometry : angle 0.63657 (14008) hydrogen bonds : bond 0.03983 ( 502) hydrogen bonds : angle 5.19076 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 ILE cc_start: 0.7557 (mt) cc_final: 0.7311 (mp) REVERT: B 110 ARG cc_start: 0.8940 (mtt-85) cc_final: 0.8543 (mtt-85) REVERT: B 120 MET cc_start: 0.7020 (mmm) cc_final: 0.6505 (mmp) REVERT: B 121 THR cc_start: 0.8330 (p) cc_final: 0.8077 (p) REVERT: A 398 ASN cc_start: 0.9461 (m-40) cc_final: 0.9069 (m-40) REVERT: A 749 ILE cc_start: 0.9273 (tt) cc_final: 0.9032 (tt) REVERT: C 107 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6939 (tm-30) outliers start: 15 outliers final: 8 residues processed: 127 average time/residue: 0.0917 time to fit residues: 17.0212 Evaluate side-chains 104 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 418 HIS ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.083760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061570 restraints weight = 31075.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063849 restraints weight = 15082.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.065379 restraints weight = 9390.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066421 restraints weight = 6786.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067098 restraints weight = 5412.296| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10372 Z= 0.114 Angle : 0.567 10.608 14008 Z= 0.289 Chirality : 0.042 0.240 1527 Planarity : 0.004 0.036 1793 Dihedral : 17.260 168.745 1427 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.57 % Allowed : 7.66 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.24), residues: 1238 helix: 1.48 (0.21), residues: 599 sheet: 0.63 (0.38), residues: 168 loop : 0.70 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.013 0.001 TYR A 711 PHE 0.013 0.001 PHE C 255 TRP 0.012 0.001 TRP A 414 HIS 0.010 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00253 (10372) covalent geometry : angle 0.56735 (14008) hydrogen bonds : bond 0.03484 ( 502) hydrogen bonds : angle 4.73551 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.8966 (mtt-85) cc_final: 0.8638 (mtt-85) REVERT: A 398 ASN cc_start: 0.9461 (m-40) cc_final: 0.9071 (m-40) REVERT: A 749 ILE cc_start: 0.9258 (tt) cc_final: 0.9023 (tt) REVERT: C 107 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: C 123 MET cc_start: 0.8779 (mmm) cc_final: 0.8402 (tpt) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.0887 time to fit residues: 15.3761 Evaluate side-chains 106 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.083950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.061690 restraints weight = 31195.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.064015 restraints weight = 14830.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065589 restraints weight = 9178.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066650 restraints weight = 6605.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067341 restraints weight = 5274.356| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10372 Z= 0.128 Angle : 0.560 11.538 14008 Z= 0.282 Chirality : 0.043 0.333 1527 Planarity : 0.004 0.037 1793 Dihedral : 16.191 169.808 1427 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.03 % Allowed : 9.23 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.24), residues: 1238 helix: 1.71 (0.21), residues: 605 sheet: 0.66 (0.39), residues: 168 loop : 0.70 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 779 TYR 0.013 0.001 TYR A 711 PHE 0.013 0.001 PHE A 586 TRP 0.010 0.001 TRP A 22 HIS 0.009 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00294 (10372) covalent geometry : angle 0.55961 (14008) hydrogen bonds : bond 0.03342 ( 502) hydrogen bonds : angle 4.61031 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8742 (mp10) cc_final: 0.8363 (mp10) REVERT: B 93 PHE cc_start: 0.8786 (m-80) cc_final: 0.8439 (m-80) REVERT: B 110 ARG cc_start: 0.8970 (mtt-85) cc_final: 0.8614 (mtt-85) REVERT: A 135 MET cc_start: 0.7925 (mmm) cc_final: 0.7621 (mmm) REVERT: A 398 ASN cc_start: 0.9459 (m-40) cc_final: 0.9060 (m-40) REVERT: C 107 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6771 (tm-30) REVERT: C 289 ILE cc_start: 0.8804 (mp) cc_final: 0.8510 (tt) REVERT: C 371 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7495 (m90) outliers start: 22 outliers final: 15 residues processed: 116 average time/residue: 0.0824 time to fit residues: 14.5585 Evaluate side-chains 107 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 0.0050 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 0.0870 chunk 8 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.083150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.061030 restraints weight = 31006.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.063307 restraints weight = 14884.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.064832 restraints weight = 9271.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065858 restraints weight = 6714.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.066529 restraints weight = 5387.080| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10372 Z= 0.131 Angle : 0.557 13.188 14008 Z= 0.278 Chirality : 0.042 0.327 1527 Planarity : 0.004 0.038 1793 Dihedral : 15.728 171.252 1427 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.85 % Allowed : 9.60 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1238 helix: 1.84 (0.21), residues: 610 sheet: 0.68 (0.39), residues: 169 loop : 0.75 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.013 0.001 TYR A 787 PHE 0.014 0.001 PHE C 255 TRP 0.009 0.001 TRP C 79 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00301 (10372) covalent geometry : angle 0.55748 (14008) hydrogen bonds : bond 0.03255 ( 502) hydrogen bonds : angle 4.52293 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8879 (mp10) cc_final: 0.8468 (mp10) REVERT: B 93 PHE cc_start: 0.8731 (m-80) cc_final: 0.8386 (m-80) REVERT: B 110 ARG cc_start: 0.8975 (mtt-85) cc_final: 0.8593 (mtt-85) REVERT: B 120 MET cc_start: 0.7219 (mpp) cc_final: 0.6885 (mpp) REVERT: A 135 MET cc_start: 0.7994 (mmm) cc_final: 0.7653 (mmm) REVERT: A 177 MET cc_start: 0.8429 (ppp) cc_final: 0.8185 (ppp) REVERT: A 398 ASN cc_start: 0.9459 (m-40) cc_final: 0.9096 (m-40) REVERT: C 227 MET cc_start: 0.9049 (tpp) cc_final: 0.8842 (ttm) REVERT: C 289 ILE cc_start: 0.8836 (mp) cc_final: 0.8565 (tt) REVERT: C 371 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7529 (m90) outliers start: 20 outliers final: 16 residues processed: 112 average time/residue: 0.0859 time to fit residues: 14.3876 Evaluate side-chains 113 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 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 = 0.3478 r_free = 0.3478 target = 0.083759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061497 restraints weight = 31348.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063807 restraints weight = 14949.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065355 restraints weight = 9243.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066395 restraints weight = 6680.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067030 restraints weight = 5334.133| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10372 Z= 0.115 Angle : 0.545 13.495 14008 Z= 0.271 Chirality : 0.041 0.315 1527 Planarity : 0.004 0.038 1793 Dihedral : 15.778 173.580 1427 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.75 % Allowed : 10.34 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.24), residues: 1238 helix: 1.89 (0.21), residues: 610 sheet: 0.72 (0.40), residues: 167 loop : 0.72 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 779 TYR 0.013 0.001 TYR A 787 PHE 0.024 0.001 PHE B 70 TRP 0.007 0.001 TRP C 79 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00264 (10372) covalent geometry : angle 0.54545 (14008) hydrogen bonds : bond 0.03121 ( 502) hydrogen bonds : angle 4.45143 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8749 (mp10) cc_final: 0.8304 (mp10) REVERT: B 93 PHE cc_start: 0.8708 (m-80) cc_final: 0.8380 (m-80) REVERT: B 110 ARG cc_start: 0.8989 (mtt-85) cc_final: 0.8594 (mtt-85) REVERT: B 120 MET cc_start: 0.7033 (mpp) cc_final: 0.6817 (mpp) REVERT: A 135 MET cc_start: 0.8054 (mmm) cc_final: 0.7716 (mmm) REVERT: A 177 MET cc_start: 0.8388 (ppp) cc_final: 0.8098 (ppp) REVERT: A 398 ASN cc_start: 0.9456 (m-40) cc_final: 0.9078 (m-40) REVERT: C 65 LEU cc_start: 0.8992 (mt) cc_final: 0.8777 (mt) REVERT: C 107 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6756 (tm-30) REVERT: C 132 MET cc_start: 0.8887 (ptm) cc_final: 0.8642 (ppp) REVERT: C 289 ILE cc_start: 0.8795 (mp) cc_final: 0.8536 (tt) REVERT: C 371 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7533 (m90) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.0839 time to fit residues: 14.2507 Evaluate side-chains 112 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 11 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 0.5090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.083765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061534 restraints weight = 30938.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063830 restraints weight = 14912.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065359 restraints weight = 9268.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066384 restraints weight = 6708.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066945 restraints weight = 5369.897| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10372 Z= 0.112 Angle : 0.539 13.711 14008 Z= 0.271 Chirality : 0.041 0.294 1527 Planarity : 0.003 0.038 1793 Dihedral : 16.040 177.621 1427 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.85 % Allowed : 11.36 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.24), residues: 1238 helix: 1.98 (0.21), residues: 604 sheet: 0.71 (0.40), residues: 167 loop : 0.77 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.012 0.001 TYR B 86 PHE 0.014 0.001 PHE A 444 TRP 0.010 0.001 TRP A 781 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00254 (10372) covalent geometry : angle 0.53864 (14008) hydrogen bonds : bond 0.03046 ( 502) hydrogen bonds : angle 4.43094 ( 1416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8629 (m-80) cc_final: 0.8308 (m-80) REVERT: B 110 ARG cc_start: 0.9028 (mtt-85) cc_final: 0.8652 (mtt-85) REVERT: B 120 MET cc_start: 0.7071 (mpp) cc_final: 0.6851 (mpp) REVERT: A 398 ASN cc_start: 0.9451 (m-40) cc_final: 0.9074 (m-40) REVERT: C 65 LEU cc_start: 0.8927 (mt) cc_final: 0.8723 (mt) REVERT: C 107 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6709 (tm-30) REVERT: C 132 MET cc_start: 0.8881 (ptm) cc_final: 0.8645 (ppp) REVERT: C 289 ILE cc_start: 0.8797 (mp) cc_final: 0.8534 (tt) REVERT: C 371 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7549 (m90) outliers start: 20 outliers final: 16 residues processed: 108 average time/residue: 0.0921 time to fit residues: 14.7818 Evaluate side-chains 107 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN ** A 464 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 = 0.3487 r_free = 0.3487 target = 0.084187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061937 restraints weight = 31121.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064234 restraints weight = 14949.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.065782 restraints weight = 9312.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.066819 restraints weight = 6728.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.067508 restraints weight = 5373.830| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10372 Z= 0.107 Angle : 0.540 13.897 14008 Z= 0.270 Chirality : 0.041 0.274 1527 Planarity : 0.003 0.038 1793 Dihedral : 16.234 178.826 1427 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.03 % Allowed : 11.73 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.25), residues: 1238 helix: 2.03 (0.22), residues: 599 sheet: 0.77 (0.40), residues: 165 loop : 0.83 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.016 0.001 TYR A 787 PHE 0.015 0.001 PHE A 444 TRP 0.007 0.001 TRP A 414 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00244 (10372) covalent geometry : angle 0.54024 (14008) hydrogen bonds : bond 0.03046 ( 502) hydrogen bonds : angle 4.42341 ( 1416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9035 (mtt-85) cc_final: 0.8663 (mtt-85) REVERT: A 134 ASP cc_start: 0.8619 (m-30) cc_final: 0.8417 (m-30) REVERT: A 398 ASN cc_start: 0.9447 (m-40) cc_final: 0.9073 (m-40) REVERT: A 442 GLU cc_start: 0.8172 (tp30) cc_final: 0.7802 (tm-30) REVERT: A 783 MET cc_start: 0.7754 (tpp) cc_final: 0.7544 (tpp) REVERT: C 107 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: C 132 MET cc_start: 0.8870 (ptm) cc_final: 0.8652 (ppp) REVERT: C 289 ILE cc_start: 0.8759 (mp) cc_final: 0.8482 (tt) REVERT: C 371 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7524 (m90) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.0830 time to fit residues: 14.5908 Evaluate side-chains 108 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 74 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 10.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 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 = 0.3452 r_free = 0.3452 target = 0.082436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060197 restraints weight = 31272.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.062449 restraints weight = 15053.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063916 restraints weight = 9371.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.064955 restraints weight = 6826.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065680 restraints weight = 5468.975| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10372 Z= 0.161 Angle : 0.583 8.407 14008 Z= 0.293 Chirality : 0.042 0.262 1527 Planarity : 0.003 0.038 1793 Dihedral : 16.276 179.289 1427 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.94 % Allowed : 11.91 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.24), residues: 1238 helix: 1.95 (0.21), residues: 605 sheet: 0.63 (0.40), residues: 169 loop : 0.63 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 92 TYR 0.014 0.001 TYR A 711 PHE 0.016 0.001 PHE A 444 TRP 0.009 0.001 TRP C 79 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00370 (10372) covalent geometry : angle 0.58259 (14008) hydrogen bonds : bond 0.03403 ( 502) hydrogen bonds : angle 4.53542 ( 1416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8718 (m-80) cc_final: 0.8493 (m-80) REVERT: B 110 ARG cc_start: 0.9057 (mtt-85) cc_final: 0.8681 (mtt-85) REVERT: A 398 ASN cc_start: 0.9459 (m-40) cc_final: 0.9077 (m-40) REVERT: A 442 GLU cc_start: 0.8184 (tp30) cc_final: 0.7796 (tm-30) REVERT: A 783 MET cc_start: 0.7807 (tpp) cc_final: 0.7500 (tpp) REVERT: C 132 MET cc_start: 0.8872 (ptm) cc_final: 0.8616 (ppp) REVERT: C 371 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7536 (m90) outliers start: 21 outliers final: 17 residues processed: 107 average time/residue: 0.0782 time to fit residues: 12.6855 Evaluate side-chains 105 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 86 optimal weight: 9.9990 chunk 23 optimal weight: 0.0270 chunk 59 optimal weight: 0.0770 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.084422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062442 restraints weight = 30266.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064783 restraints weight = 14478.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.066345 restraints weight = 8898.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067418 restraints weight = 6394.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.068103 restraints weight = 5063.274| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10372 Z= 0.100 Angle : 0.553 10.421 14008 Z= 0.275 Chirality : 0.041 0.237 1527 Planarity : 0.003 0.038 1793 Dihedral : 16.293 179.638 1427 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.48 % Allowed : 12.37 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.25), residues: 1238 helix: 2.05 (0.22), residues: 600 sheet: 0.80 (0.40), residues: 167 loop : 0.65 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 92 TYR 0.011 0.001 TYR A 787 PHE 0.013 0.001 PHE A 444 TRP 0.007 0.001 TRP A 414 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00225 (10372) covalent geometry : angle 0.55301 (14008) hydrogen bonds : bond 0.02944 ( 502) hydrogen bonds : angle 4.34941 ( 1416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8642 (m-80) cc_final: 0.8409 (m-80) REVERT: B 110 ARG cc_start: 0.9070 (mtt-85) cc_final: 0.8717 (mtt-85) REVERT: A 398 ASN cc_start: 0.9462 (m-40) cc_final: 0.9093 (m-40) REVERT: A 442 GLU cc_start: 0.8148 (tp30) cc_final: 0.7742 (tm-30) REVERT: A 783 MET cc_start: 0.7719 (tpp) cc_final: 0.7509 (tpp) REVERT: C 107 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: C 132 MET cc_start: 0.8877 (ptm) cc_final: 0.8664 (ppp) REVERT: C 289 ILE cc_start: 0.8679 (mp) cc_final: 0.8407 (tt) REVERT: C 371 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7516 (m90) outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 0.0831 time to fit residues: 13.0673 Evaluate side-chains 100 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 79 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 112 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 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 = 0.3462 r_free = 0.3462 target = 0.083359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061102 restraints weight = 30627.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.063390 restraints weight = 14903.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.064934 restraints weight = 9285.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065995 restraints weight = 6715.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066649 restraints weight = 5350.668| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10372 Z= 0.128 Angle : 0.580 10.174 14008 Z= 0.288 Chirality : 0.042 0.229 1527 Planarity : 0.003 0.038 1793 Dihedral : 16.230 179.970 1427 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.48 % Allowed : 12.28 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.25), residues: 1238 helix: 2.00 (0.22), residues: 606 sheet: 0.76 (0.41), residues: 169 loop : 0.57 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 92 TYR 0.011 0.001 TYR B 86 PHE 0.013 0.001 PHE A 444 TRP 0.009 0.001 TRP C 79 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00297 (10372) covalent geometry : angle 0.57980 (14008) hydrogen bonds : bond 0.03119 ( 502) hydrogen bonds : angle 4.39557 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1882.11 seconds wall clock time: 33 minutes 7.60 seconds (1987.60 seconds total)