Starting phenix.real_space_refine on Thu Aug 6 23:33:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8by2_16319/08_2026/8by2_16319_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8by2_16319/08_2026/8by2_16319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8by2_16319/08_2026/8by2_16319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8by2_16319/08_2026/8by2_16319.map" model { file = "/net/cci-nas-00/data/ceres_data/8by2_16319/08_2026/8by2_16319_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8by2_16319/08_2026/8by2_16319_trim.cif" } resolution = 3.18 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= 0.017 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 K 2 8.98 5 P 4 5.49 5 S 56 5.16 5 C 5572 2.51 5 N 1433 2.21 5 O 1487 1.98 5 H 8832 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17386 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8598 Classifications: {'peptide': 548} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 529} Chain breaks: 1 Chain: "B" Number of atoms: 8568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8568 Classifications: {'peptide': 546} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {' K': 1, 'AMP%rna2p': 1, 'GSH': 1, 'PGW': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {' K': 1, 'AMP%rna2p': 1, 'GSH': 1, 'PGW': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Time building chain proxies: 2.98, per 1000 atoms: 0.17 Number of scatterers: 17386 At special positions: 0 Unit cell: (93.03, 73.538, 110.75, 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) K 2 19.00 S 56 16.00 P 4 15.00 O 1487 8.00 N 1433 7.00 C 5572 6.00 H 8832 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 432.1 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 78.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 29 through 42 Processing helix chain 'A' and resid 53 through 72 Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 82 through 109 removed outlier: 4.369A pdb=" N ALA A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.727A pdb=" N GLU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 142 through 171 removed outlier: 4.362A pdb=" N ILE A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.893A pdb=" N ILE A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Proline residue: A 167 - end of helix removed outlier: 3.818A pdb=" N THR A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 178 through 183 removed outlier: 4.160A pdb=" N LEU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.533A pdb=" N ARG A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.590A pdb=" N VAL A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.602A pdb=" N GLY A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 283 Proline residue: A 267 - end of helix removed outlier: 4.114A pdb=" N GLY A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 316 removed outlier: 3.681A pdb=" N LEU A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG A 316 " --> pdb=" O TRP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.849A pdb=" N PHE A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.877A pdb=" N VAL A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 370 Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.689A pdb=" N LEU A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 419 removed outlier: 3.558A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 439 removed outlier: 3.510A pdb=" N HIS A 434 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A 436 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG A 439 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 536 through 560 removed outlier: 3.645A pdb=" N MET A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 19 Processing helix chain 'B' and resid 19 through 27 removed outlier: 3.550A pdb=" N ALA B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 51 through 72 removed outlier: 3.954A pdb=" N ILE B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 89 through 109 removed outlier: 3.734A pdb=" N GLN B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.860A pdb=" N GLU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 142 through 165 removed outlier: 4.265A pdb=" N ILE B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.512A pdb=" N LEU B 169 " --> pdb=" O MET B 165 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 176 through 202 removed outlier: 3.795A pdb=" N ALA B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 217 through 236 removed outlier: 3.749A pdb=" N GLU B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.633A pdb=" N GLY B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'B' and resid 270 through 284 removed outlier: 4.252A pdb=" N PHE B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 292 through 316 removed outlier: 3.876A pdb=" N ILE B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG B 316 " --> pdb=" O TRP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 333 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.808A pdb=" N VAL B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 370 Processing helix chain 'B' and resid 370 through 383 removed outlier: 3.783A pdb=" N LEU B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 420 removed outlier: 3.865A pdb=" N ILE B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 4.090A pdb=" N LYS B 440 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 4.247A pdb=" N LEU B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 457' Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 473 through 488 Processing helix chain 'B' and resid 499 through 510 removed outlier: 3.600A pdb=" N ARG B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 534 Processing helix chain 'B' and resid 536 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 447 removed outlier: 3.687A pdb=" N LYS A 444 " --> pdb=" O MET A 425 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 402 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU A 428 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A 404 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 497 Processing sheet with id=AA3, first strand: chain 'B' and resid 444 through 447 removed outlier: 4.075A pdb=" N LYS B 444 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 466 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 496 through 497 572 hydrogen bonds defined for protein. 1701 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: 3.46 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8800 1.03 - 1.23: 38 1.23 - 1.42: 3428 1.42 - 1.62: 5156 1.62 - 1.81: 108 Bond restraints: 17530 Sorted by residual: bond pdb=" N2 GSH B 603 " pdb=" HN2 GSH B 603 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" N3 GSH A 603 " pdb=" HN3 GSH A 603 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" N2 GSH A 603 " pdb=" HN2 GSH A 603 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" N3 GSH B 603 " pdb=" HN3 GSH B 603 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" N1 GSH B 603 " pdb="HN11 GSH B 603 " ideal model delta sigma weight residual 0.890 1.037 -0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 17525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 29965 1.13 - 2.26: 1667 2.26 - 3.39: 102 3.39 - 4.52: 31 4.52 - 5.65: 12 Bond angle restraints: 31777 Sorted by residual: angle pdb=" N VAL B 86 " pdb=" CA VAL B 86 " pdb=" C VAL B 86 " ideal model delta sigma weight residual 113.53 109.10 4.43 9.80e-01 1.04e+00 2.04e+01 angle pdb=" CA VAL B 86 " pdb=" C VAL B 86 " pdb=" N PHE B 87 " ideal model delta sigma weight residual 119.31 116.80 2.51 1.15e+00 7.56e-01 4.76e+00 angle pdb=" C ILE B 40 " pdb=" CA ILE B 40 " pdb=" CB ILE B 40 " ideal model delta sigma weight residual 112.26 108.76 3.50 1.62e+00 3.81e-01 4.67e+00 angle pdb=" N THR A 177 " pdb=" CA THR A 177 " pdb=" CB THR A 177 " ideal model delta sigma weight residual 114.17 111.89 2.28 1.14e+00 7.69e-01 3.99e+00 angle pdb=" N ILE B 41 " pdb=" CA ILE B 41 " pdb=" C ILE B 41 " ideal model delta sigma weight residual 111.91 110.14 1.77 8.90e-01 1.26e+00 3.94e+00 ... (remaining 31772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 7730 35.00 - 70.00: 400 70.00 - 105.01: 24 105.01 - 140.01: 3 140.01 - 175.01: 4 Dihedral angle restraints: 8161 sinusoidal: 4589 harmonic: 3572 Sorted by residual: dihedral pdb=" C5' AMP B 602 " pdb=" O5' AMP B 602 " pdb=" P AMP B 602 " pdb=" O3P AMP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 66.55 -126.54 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" O01 PGW B 604 " pdb=" C01 PGW B 604 " pdb=" C02 PGW B 604 " pdb=" O03 PGW B 604 " ideal model delta sinusoidal sigma weight residual 59.30 -115.71 175.01 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C03 PGW B 604 " pdb=" C01 PGW B 604 " pdb=" C02 PGW B 604 " pdb=" O03 PGW B 604 " ideal model delta sinusoidal sigma weight residual 295.35 120.45 174.90 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 978 0.026 - 0.052: 245 0.052 - 0.078: 106 0.078 - 0.105: 50 0.105 - 0.131: 17 Chirality restraints: 1396 Sorted by residual: chirality pdb=" CA ILE A 494 " pdb=" N ILE A 494 " pdb=" C ILE A 494 " pdb=" CB ILE A 494 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA VAL A 320 " pdb=" N VAL A 320 " pdb=" C VAL A 320 " pdb=" CB VAL A 320 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1393 not shown) Planarity restraints: 2512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GSH A 603 " 0.003 2.00e-02 2.50e+03 3.95e-02 2.34e+01 pdb=" CA2 GSH A 603 " 0.047 2.00e-02 2.50e+03 pdb=" CA3 GSH A 603 " 0.050 2.00e-02 2.50e+03 pdb=" N3 GSH A 603 " -0.004 2.00e-02 2.50e+03 pdb=" O2 GSH A 603 " -0.043 2.00e-02 2.50e+03 pdb=" HN3 GSH A 603 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG1 GSH B 603 " -0.031 2.00e-02 2.50e+03 2.40e-02 8.66e+00 pdb=" CD1 GSH B 603 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GSH B 603 " 0.023 2.00e-02 2.50e+03 pdb=" CA2 GSH B 603 " -0.032 2.00e-02 2.50e+03 pdb=" N2 GSH B 603 " 0.006 2.00e-02 2.50e+03 pdb=" HN2 GSH B 603 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 316 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO B 317 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " 0.037 5.00e-02 4.00e+02 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.32: 4109 2.32 - 3.02: 47181 3.02 - 3.73: 60784 3.73 - 4.43: 91549 4.43 - 5.14: 145457 Nonbonded interactions: 349080 Sorted by model distance: nonbonded pdb=" OE1 GLN A 93 " pdb="HE22 GLN A 155 " model vdw 1.609 2.450 nonbonded pdb=" OD1 ASP A 51 " pdb=" H SER A 54 " model vdw 1.634 2.450 nonbonded pdb=" O ARG B 212 " pdb=" HE ARG B 212 " model vdw 1.651 2.450 nonbonded pdb=" OD1 ASP B 429 " pdb=" H HIS B 430 " model vdw 1.656 2.450 nonbonded pdb=" OE1 GLU A 512 " pdb=" H GLU A 512 " model vdw 1.662 2.450 ... (remaining 349075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 385 or resid 400 through 604)) selection = (chain 'B' and (resid 1 through 126 or (resid 127 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 128 through 604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.790 Find NCS groups from input model: 0.280 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.002 0.025 8698 Z= 0.113 Angle : 0.533 5.649 11751 Z= 0.265 Chirality : 0.034 0.131 1396 Planarity : 0.004 0.066 1457 Dihedral : 19.761 175.012 3244 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 24.83 % Favored : 75.17 % 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 (0.27), residues: 1086 helix: 2.27 (0.19), residues: 799 sheet: -0.61 (0.64), residues: 60 loop : -2.29 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 208 TYR 0.019 0.001 TYR A 538 PHE 0.008 0.001 PHE A 410 TRP 0.007 0.001 TRP B 44 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8698) covalent geometry : angle 0.53271 / 0.27 (11751) hydrogen bonds : bond 0.06895 / 5.08 ( 572) hydrogen bonds : angle 4.08771 / 2.99 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.380 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1624 time to fit residues: 31.8934 Evaluate side-chains 131 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112267 restraints weight = 35589.715| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.76 r_work: 0.3217 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8698 Z= 0.147 Angle : 0.525 5.781 11751 Z= 0.262 Chirality : 0.034 0.135 1396 Planarity : 0.004 0.058 1457 Dihedral : 15.361 175.080 1322 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.38 % Allowed : 24.14 % Favored : 74.48 % 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: 1.69 (0.27), residues: 1086 helix: 2.14 (0.19), residues: 800 sheet: -0.60 (0.64), residues: 60 loop : -2.30 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 496 TYR 0.015 0.002 TYR B 257 PHE 0.009 0.001 PHE A 410 TRP 0.011 0.001 TRP B 44 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 8698) covalent geometry : angle 0.52532 / 0.26 (11751) hydrogen bonds : bond 0.03827 / 2.58 ( 572) hydrogen bonds : angle 3.76619 / 2.79 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.503 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 138 average time/residue: 0.2296 time to fit residues: 44.0054 Evaluate side-chains 138 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 94 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.140208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113829 restraints weight = 35580.895| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.78 r_work: 0.3243 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8698 Z= 0.099 Angle : 0.501 5.927 11751 Z= 0.245 Chirality : 0.034 0.143 1396 Planarity : 0.004 0.054 1457 Dihedral : 14.740 174.622 1322 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.26 % Allowed : 24.14 % Favored : 74.60 % 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: 1.79 (0.27), residues: 1086 helix: 2.21 (0.19), residues: 800 sheet: -0.66 (0.64), residues: 60 loop : -2.22 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 439 TYR 0.015 0.001 TYR B 257 PHE 0.009 0.001 PHE A 410 TRP 0.008 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 8698) covalent geometry : angle 0.50147 / 0.24 (11751) hydrogen bonds : bond 0.03414 / 2.30 ( 572) hydrogen bonds : angle 3.65289 / 2.71 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 MET cc_start: 0.7888 (tpp) cc_final: 0.7576 (mmt) outliers start: 11 outliers final: 10 residues processed: 143 average time/residue: 0.1903 time to fit residues: 39.1951 Evaluate side-chains 143 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113910 restraints weight = 35443.021| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.80 r_work: 0.3237 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8698 Z= 0.105 Angle : 0.506 5.877 11751 Z= 0.247 Chirality : 0.034 0.141 1396 Planarity : 0.004 0.052 1457 Dihedral : 14.376 174.601 1322 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.95 % Allowed : 23.45 % Favored : 74.60 % 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: 1.76 (0.27), residues: 1086 helix: 2.19 (0.19), residues: 800 sheet: -0.63 (0.64), residues: 60 loop : -2.21 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 439 TYR 0.010 0.001 TYR B 257 PHE 0.008 0.001 PHE A 410 TRP 0.009 0.001 TRP B 44 HIS 0.002 0.000 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 8698) covalent geometry : angle 0.50564 / 0.25 (11751) hydrogen bonds : bond 0.03421 / 2.32 ( 572) hydrogen bonds : angle 3.65315 / 2.71 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.6913 (tt) cc_final: 0.6689 (tp) outliers start: 17 outliers final: 14 residues processed: 147 average time/residue: 0.1818 time to fit residues: 38.5294 Evaluate side-chains 143 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114154 restraints weight = 35338.989| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.76 r_work: 0.3253 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8698 Z= 0.098 Angle : 0.501 5.893 11751 Z= 0.244 Chirality : 0.034 0.142 1396 Planarity : 0.004 0.051 1457 Dihedral : 13.932 174.473 1322 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.49 % Allowed : 23.91 % Favored : 74.60 % 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 (0.27), residues: 1086 helix: 2.24 (0.19), residues: 801 sheet: -0.65 (0.63), residues: 60 loop : -2.19 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 439 TYR 0.008 0.001 TYR B 257 PHE 0.008 0.001 PHE A 410 TRP 0.008 0.001 TRP B 44 HIS 0.002 0.000 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 8698) covalent geometry : angle 0.50109 / 0.24 (11751) hydrogen bonds : bond 0.03283 / 2.22 ( 572) hydrogen bonds : angle 3.62517 / 2.68 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 141 average time/residue: 0.1795 time to fit residues: 36.1742 Evaluate side-chains 142 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.0070 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114033 restraints weight = 35059.474| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.76 r_work: 0.3247 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8698 Z= 0.100 Angle : 0.498 5.763 11751 Z= 0.243 Chirality : 0.034 0.142 1396 Planarity : 0.004 0.053 1457 Dihedral : 13.464 174.667 1322 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.61 % Allowed : 23.79 % Favored : 74.60 % 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: 1.86 (0.27), residues: 1086 helix: 2.25 (0.19), residues: 801 sheet: -0.63 (0.63), residues: 60 loop : -2.17 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 439 TYR 0.012 0.001 TYR B 257 PHE 0.008 0.001 PHE A 410 TRP 0.008 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 8698) covalent geometry : angle 0.49798 / 0.24 (11751) hydrogen bonds : bond 0.03267 / 2.20 ( 572) hydrogen bonds : angle 3.62261 / 2.68 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.6892 (tt) cc_final: 0.6656 (tp) outliers start: 14 outliers final: 12 residues processed: 141 average time/residue: 0.1947 time to fit residues: 39.4445 Evaluate side-chains 144 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111801 restraints weight = 35383.476| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.76 r_work: 0.3200 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8698 Z= 0.142 Angle : 0.530 5.908 11751 Z= 0.262 Chirality : 0.034 0.140 1396 Planarity : 0.004 0.059 1457 Dihedral : 13.164 175.663 1322 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.84 % Allowed : 23.22 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.27), residues: 1086 helix: 2.12 (0.19), residues: 800 sheet: -0.66 (0.64), residues: 60 loop : -2.23 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 439 TYR 0.011 0.002 TYR A 201 PHE 0.010 0.001 PHE B 328 TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 8698) covalent geometry : angle 0.52951 / 0.26 (11751) hydrogen bonds : bond 0.03842 / 2.58 ( 572) hydrogen bonds : angle 3.76304 / 2.78 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.4629 (OUTLIER) cc_final: 0.4123 (mp) REVERT: B 216 ARG cc_start: 0.6992 (ptt90) cc_final: 0.6773 (ptm160) outliers start: 16 outliers final: 12 residues processed: 145 average time/residue: 0.2068 time to fit residues: 42.4717 Evaluate side-chains 146 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 8 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.139778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113328 restraints weight = 35457.162| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.77 r_work: 0.3233 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8698 Z= 0.098 Angle : 0.508 5.646 11751 Z= 0.248 Chirality : 0.034 0.145 1396 Planarity : 0.004 0.060 1457 Dihedral : 12.921 174.907 1322 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.61 % Allowed : 23.33 % Favored : 75.06 % 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: 1.78 (0.27), residues: 1086 helix: 2.18 (0.19), residues: 806 sheet: -0.59 (0.64), residues: 60 loop : -2.26 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 439 TYR 0.011 0.001 TYR B 257 PHE 0.009 0.001 PHE A 410 TRP 0.009 0.001 TRP B 44 HIS 0.002 0.000 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 8698) covalent geometry : angle 0.50835 / 0.25 (11751) hydrogen bonds : bond 0.03344 / 2.25 ( 572) hydrogen bonds : angle 3.65303 / 2.70 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.7997 (tmm160) cc_final: 0.7683 (ttp-110) outliers start: 14 outliers final: 12 residues processed: 142 average time/residue: 0.1646 time to fit residues: 33.4316 Evaluate side-chains 144 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 83 optimal weight: 0.0870 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112203 restraints weight = 35507.852| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.77 r_work: 0.3226 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8698 Z= 0.126 Angle : 0.526 5.812 11751 Z= 0.258 Chirality : 0.034 0.142 1396 Planarity : 0.004 0.066 1457 Dihedral : 12.881 175.301 1322 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.61 % Allowed : 23.45 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.27), residues: 1086 helix: 2.15 (0.19), residues: 800 sheet: -0.58 (0.65), residues: 60 loop : -2.22 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 439 TYR 0.011 0.001 TYR B 257 PHE 0.009 0.001 PHE A 410 TRP 0.009 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8698) covalent geometry : angle 0.52561 / 0.26 (11751) hydrogen bonds : bond 0.03601 / 2.44 ( 572) hydrogen bonds : angle 3.71638 / 2.75 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 258 ARG cc_start: 0.8021 (tmm160) cc_final: 0.7714 (ttp-110) outliers start: 14 outliers final: 13 residues processed: 141 average time/residue: 0.1943 time to fit residues: 39.3609 Evaluate side-chains 147 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114056 restraints weight = 35561.978| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.72 r_work: 0.3255 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8698 Z= 0.098 Angle : 0.515 5.648 11751 Z= 0.251 Chirality : 0.034 0.144 1396 Planarity : 0.004 0.070 1457 Dihedral : 12.760 175.017 1322 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.49 % Allowed : 23.68 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.27), residues: 1086 helix: 2.22 (0.19), residues: 800 sheet: -0.55 (0.64), residues: 60 loop : -2.19 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 439 TYR 0.011 0.001 TYR B 257 PHE 0.008 0.001 PHE A 410 TRP 0.009 0.001 TRP B 44 HIS 0.002 0.000 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 8698) covalent geometry : angle 0.51450 / 0.25 (11751) hydrogen bonds : bond 0.03303 / 2.24 ( 572) hydrogen bonds : angle 3.65043 / 2.70 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.8022 (tmm160) cc_final: 0.7726 (ttp-110) outliers start: 13 outliers final: 12 residues processed: 144 average time/residue: 0.1904 time to fit residues: 38.5555 Evaluate side-chains 146 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 103 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.139514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113292 restraints weight = 35877.206| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.74 r_work: 0.3248 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8698 Z= 0.114 Angle : 0.527 6.619 11751 Z= 0.258 Chirality : 0.034 0.143 1396 Planarity : 0.005 0.092 1457 Dihedral : 12.739 175.425 1322 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.61 % Allowed : 23.45 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.27), residues: 1086 helix: 2.18 (0.19), residues: 800 sheet: -0.54 (0.65), residues: 60 loop : -2.23 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 439 TYR 0.014 0.001 TYR A 257 PHE 0.008 0.001 PHE A 410 TRP 0.008 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 8698) covalent geometry : angle 0.52701 / 0.26 (11751) hydrogen bonds : bond 0.03459 / 2.35 ( 572) hydrogen bonds : angle 3.69082 / 2.73 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.28 seconds wall clock time: 59 minutes 7.27 seconds (3547.27 seconds total)