Starting phenix.real_space_refine on Sun Aug 24 07:28:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8by2_16319/08_2025/8by2_16319_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8by2_16319/08_2025/8by2_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_2025/8by2_16319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8by2_16319/08_2025/8by2_16319.map" model { file = "/net/cci-nas-00/data/ceres_data/8by2_16319/08_2025/8by2_16319_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8by2_16319/08_2025/8by2_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 8802 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17356 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: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 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: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 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: 3.15, per 1000 atoms: 0.18 Number of scatterers: 17356 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 8802 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: 2.23 Conformation dependent library (CDL) restraints added in 555.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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 78.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 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: 3.98 Time building geometry restraints manager: 1.62 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: 8796 1.03 - 1.23: 14 1.23 - 1.42: 3426 1.42 - 1.62: 5156 1.62 - 1.81: 108 Bond restraints: 17500 Sorted by residual: bond pdb=" C1 GSH B 603 " pdb=" O11 GSH B 603 " ideal model delta sigma weight residual 1.213 1.247 -0.034 1.00e-02 1.00e+04 1.16e+01 bond pdb=" C1 GSH A 603 " pdb=" O11 GSH A 603 " ideal model delta sigma weight residual 1.213 1.247 -0.034 1.00e-02 1.00e+04 1.15e+01 bond pdb=" C1 GSH B 603 " pdb=" O12 GSH B 603 " ideal model delta sigma weight residual 1.307 1.247 0.060 1.90e-02 2.77e+03 1.00e+01 bond pdb=" C1 GSH A 603 " pdb=" O12 GSH A 603 " ideal model delta sigma weight residual 1.307 1.247 0.060 1.90e-02 2.77e+03 9.98e+00 bond pdb=" C3 GSH A 603 " pdb=" O32 GSH A 603 " ideal model delta sigma weight residual 1.308 1.246 0.062 2.00e-02 2.50e+03 9.56e+00 ... (remaining 17495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 31483 1.92 - 3.84: 180 3.84 - 5.76: 40 5.76 - 7.67: 3 7.67 - 9.59: 3 Bond angle restraints: 31709 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=" C1' AMP B 602 " pdb=" C2' AMP B 602 " pdb=" C3' AMP B 602 " ideal model delta sigma weight residual 111.00 101.41 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C1' AMP A 602 " pdb=" C2' AMP A 602 " pdb=" C3' AMP A 602 " ideal model delta sigma weight residual 111.00 101.56 9.44 3.00e+00 1.11e-01 9.91e+00 angle pdb=" CA3 GSH B 603 " pdb=" C3 GSH B 603 " pdb=" O31 GSH B 603 " ideal model delta sigma weight residual 123.68 117.02 6.66 2.25e+00 1.97e-01 8.75e+00 angle pdb=" CA3 GSH A 603 " pdb=" C3 GSH A 603 " pdb=" O31 GSH A 603 " ideal model delta sigma weight residual 123.68 117.11 6.57 2.25e+00 1.97e-01 8.51e+00 ... (remaining 31704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 7709 35.00 - 70.00: 393 70.00 - 105.01: 22 105.01 - 140.01: 3 140.01 - 175.01: 4 Dihedral angle restraints: 8131 sinusoidal: 4559 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 8128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1138 0.040 - 0.080: 187 0.080 - 0.121: 65 0.121 - 0.161: 4 0.161 - 0.201: 2 Chirality restraints: 1396 Sorted by residual: chirality pdb=" C3' AMP B 602 " pdb=" C2' AMP B 602 " pdb=" C4' AMP B 602 " pdb=" O3' AMP B 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C3' AMP A 602 " pdb=" C2' AMP A 602 " pdb=" C4' AMP A 602 " pdb=" O3' AMP A 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.98e-01 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 ... (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 2.41e-02 7.25e+00 pdb=" CA2 GSH A 603 " 0.021 2.00e-02 2.50e+03 pdb=" CA3 GSH A 603 " 0.029 2.00e-02 2.50e+03 pdb=" N3 GSH A 603 " -0.039 2.00e-02 2.50e+03 pdb=" O2 GSH A 603 " -0.008 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 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 302 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C GLY A 302 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY A 302 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE A 303 " -0.012 2.00e-02 2.50e+03 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.32: 4096 2.32 - 3.02: 47036 3.02 - 3.73: 60637 3.73 - 4.43: 91336 4.43 - 5.14: 145154 Nonbonded interactions: 348259 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 348254 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: 2.300 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: 0.070 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.220 Find NCS groups from input model: 0.210 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8698 Z= 0.152 Angle : 0.581 9.593 11751 Z= 0.280 Chirality : 0.035 0.201 1396 Planarity : 0.004 0.066 1457 Dihedral : 19.608 175.012 3240 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 aren 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 covalent geometry : bond 0.00281 ( 8698) covalent geometry : angle 0.58130 (11751) hydrogen bonds : bond 0.06895 ( 572) hydrogen bonds : angle 4.08771 ( 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 : 0.394 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1583 time to fit residues: 31.0052 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 : 0.370 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112264 restraints weight = 35432.653| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.79 r_work: 0.3209 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0428 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= 0.149 Angle : 0.543 6.306 11751 Z= 0.267 Chirality : 0.035 0.141 1396 Planarity : 0.004 0.058 1457 Dihedral : 14.454 175.268 1318 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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 aren not related in a simple way. whole: 1.64 (0.27), residues: 1086 helix: 2.11 (0.19), residues: 800 sheet: -0.62 (0.64), residues: 60 loop : -2.31 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 496 TYR 0.016 0.002 TYR B 257 PHE 0.010 0.001 PHE A 410 TRP 0.011 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8698) covalent geometry : angle 0.54281 (11751) hydrogen bonds : bond 0.03860 ( 572) hydrogen bonds : angle 3.78236 ( 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 144 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.454 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 139 average time/residue: 0.1952 time to fit residues: 37.2743 Evaluate side-chains 141 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 61 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112282 restraints weight = 35666.631| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.80 r_work: 0.3217 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0513 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= 0.128 Angle : 0.529 6.108 11751 Z= 0.257 Chirality : 0.035 0.142 1396 Planarity : 0.004 0.054 1457 Dihedral : 14.084 175.239 1318 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.49 % Allowed : 23.56 % 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 aren not related in a simple way. whole: 1.63 (0.27), residues: 1086 helix: 2.10 (0.19), residues: 800 sheet: -0.71 (0.63), residues: 60 loop : -2.32 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 496 TYR 0.014 0.001 TYR B 257 PHE 0.009 0.001 PHE A 410 TRP 0.011 0.001 TRP B 44 HIS 0.002 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8698) covalent geometry : angle 0.52880 (11751) hydrogen bonds : bond 0.03789 ( 572) hydrogen bonds : angle 3.75494 ( 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 151 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 144 average time/residue: 0.1947 time to fit residues: 39.4479 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 : 0.333 ------------------------------------------------------------------------------- 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 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 13 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 348 MET 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 85 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110819 restraints weight = 35671.483| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.77 r_work: 0.3209 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8698 Z= 0.146 Angle : 0.547 6.269 11751 Z= 0.268 Chirality : 0.035 0.146 1396 Planarity : 0.004 0.053 1457 Dihedral : 13.767 175.374 1318 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.41 % Allowed : 22.64 % 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 aren not related in a simple way. whole: 1.50 (0.27), residues: 1086 helix: 2.00 (0.19), residues: 800 sheet: -0.68 (0.64), residues: 60 loop : -2.34 (0.38), residues: 226 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 0.009 0.001 PHE B 328 TRP 0.011 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8698) covalent geometry : angle 0.54668 (11751) hydrogen bonds : bond 0.03995 ( 572) hydrogen bonds : angle 3.82970 ( 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 157 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.8350 (tp30) cc_final: 0.8098 (tp30) REVERT: A 289 LEU cc_start: 0.4685 (OUTLIER) cc_final: 0.4192 (mp) REVERT: B 216 ARG cc_start: 0.7018 (ptt90) cc_final: 0.6791 (ptm160) outliers start: 21 outliers final: 16 residues processed: 148 average time/residue: 0.1872 time to fit residues: 38.9179 Evaluate side-chains 149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 13 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 348 MET Chi-restraints excluded: chain B residue 367 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 84 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112464 restraints weight = 35454.113| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.77 r_work: 0.3233 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8698 Z= 0.106 Angle : 0.531 6.156 11751 Z= 0.256 Chirality : 0.035 0.145 1396 Planarity : 0.004 0.051 1457 Dihedral : 13.368 174.650 1318 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.07 % Allowed : 23.10 % 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 aren not related in a simple way. whole: 1.63 (0.27), residues: 1086 helix: 2.10 (0.19), residues: 800 sheet: -0.70 (0.62), residues: 60 loop : -2.29 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 covalent geometry : bond 0.00234 ( 8698) covalent geometry : angle 0.53101 (11751) hydrogen bonds : bond 0.03573 ( 572) hydrogen bonds : angle 3.72411 ( 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 155 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 ARG cc_start: 0.6907 (ptt90) cc_final: 0.6702 (ptm160) outliers start: 18 outliers final: 16 residues processed: 146 average time/residue: 0.1958 time to fit residues: 39.5410 Evaluate side-chains 148 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 B residue 13 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 255 SER Chi-restraints excluded: chain B residue 348 MET 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 50 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 45 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114049 restraints weight = 35078.569| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.77 r_work: 0.3249 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8698 Z= 0.094 Angle : 0.523 6.664 11751 Z= 0.250 Chirality : 0.034 0.143 1396 Planarity : 0.004 0.055 1457 Dihedral : 12.880 174.165 1318 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.72 % Allowed : 23.45 % 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 aren not related in a simple way. whole: 1.78 (0.27), residues: 1086 helix: 2.22 (0.19), residues: 801 sheet: -0.72 (0.61), residues: 60 loop : -2.27 (0.39), residues: 225 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 0.008 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 covalent geometry : bond 0.00205 ( 8698) covalent geometry : angle 0.52276 (11751) hydrogen bonds : bond 0.03233 ( 572) hydrogen bonds : angle 3.63657 ( 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 149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.6912 (tt) cc_final: 0.6685 (tp) outliers start: 15 outliers final: 13 residues processed: 141 average time/residue: 0.1748 time to fit residues: 34.4079 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 : 0.421 ------------------------------------------------------------------------------- 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 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 13 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 255 SER Chi-restraints excluded: chain B residue 496 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3693 r_free = 0.3693 target = 0.139010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112032 restraints weight = 35307.446| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.77 r_work: 0.3218 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8698 Z= 0.128 Angle : 0.537 6.368 11751 Z= 0.260 Chirality : 0.035 0.142 1396 Planarity : 0.004 0.056 1457 Dihedral : 12.728 175.043 1318 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.84 % Allowed : 23.56 % 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 aren not related in a simple way. whole: 1.67 (0.27), residues: 1086 helix: 2.13 (0.19), residues: 800 sheet: -0.65 (0.63), residues: 60 loop : -2.26 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 439 TYR 0.010 0.001 TYR B 257 PHE 0.009 0.001 PHE A 410 TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8698) covalent geometry : angle 0.53692 (11751) hydrogen bonds : bond 0.03627 ( 572) hydrogen bonds : angle 3.73476 ( 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 150 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 216 ARG cc_start: 0.7057 (ptt90) cc_final: 0.6805 (ptm160) outliers start: 16 outliers final: 16 residues processed: 142 average time/residue: 0.1787 time to fit residues: 35.2391 Evaluate side-chains 149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 13 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 255 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3697 r_free = 0.3697 target = 0.139401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111968 restraints weight = 35254.731| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.80 r_work: 0.3203 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0852 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= 0.125 Angle : 0.543 6.389 11751 Z= 0.262 Chirality : 0.035 0.143 1396 Planarity : 0.004 0.064 1457 Dihedral : 12.609 175.224 1318 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.95 % Allowed : 23.68 % Favored : 74.37 % 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 aren not related in a simple way. whole: 1.61 (0.27), residues: 1086 helix: 2.07 (0.19), residues: 806 sheet: -0.60 (0.64), residues: 60 loop : -2.35 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 439 TYR 0.010 0.001 TYR B 257 PHE 0.009 0.001 PHE A 410 TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8698) covalent geometry : angle 0.54285 (11751) hydrogen bonds : bond 0.03663 ( 572) hydrogen bonds : angle 3.75201 ( 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 150 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 MET cc_start: 0.6924 (tpt) cc_final: 0.6674 (tpt) outliers start: 17 outliers final: 13 residues processed: 142 average time/residue: 0.1894 time to fit residues: 36.9331 Evaluate side-chains 145 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 13 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 255 SER 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 24 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3711 r_free = 0.3711 target = 0.140150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113283 restraints weight = 35550.622| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.76 r_work: 0.3230 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0847 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= 0.104 Angle : 0.533 6.262 11751 Z= 0.256 Chirality : 0.035 0.144 1396 Planarity : 0.004 0.067 1457 Dihedral : 12.413 174.868 1318 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.72 % Allowed : 24.02 % Favored : 74.25 % 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 aren not related in a simple way. whole: 1.73 (0.27), residues: 1086 helix: 2.17 (0.19), residues: 800 sheet: -0.58 (0.64), residues: 60 loop : -2.25 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 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 487 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8698) covalent geometry : angle 0.53263 (11751) hydrogen bonds : bond 0.03420 ( 572) hydrogen bonds : angle 3.69551 ( 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 149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.8057 (tmm160) cc_final: 0.7753 (ttp-110) REVERT: A 560 MET cc_start: 0.6972 (tpt) cc_final: 0.6729 (tpt) outliers start: 15 outliers final: 15 residues processed: 140 average time/residue: 0.1642 time to fit residues: 32.5970 Evaluate side-chains 148 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 13 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 255 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 484 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 57 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3685 r_free = 0.3685 target = 0.137872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111913 restraints weight = 35581.932| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.70 r_work: 0.3219 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0902 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= 0.126 Angle : 0.548 6.377 11751 Z= 0.266 Chirality : 0.035 0.169 1396 Planarity : 0.004 0.071 1457 Dihedral : 12.179 175.277 1318 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.84 % Allowed : 24.25 % Favored : 73.91 % 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 aren not related in a simple way. whole: 1.63 (0.27), residues: 1086 helix: 2.09 (0.19), residues: 800 sheet: -0.54 (0.65), residues: 60 loop : -2.28 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 439 TYR 0.010 0.001 TYR A 257 PHE 0.009 0.001 PHE A 410 TRP 0.009 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8698) covalent geometry : angle 0.54844 (11751) hydrogen bonds : bond 0.03678 ( 572) hydrogen bonds : angle 3.76076 ( 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 147 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 ARG cc_start: 0.8081 (tmm160) cc_final: 0.7781 (ttp-110) REVERT: A 560 MET cc_start: 0.7021 (tpt) cc_final: 0.6783 (tpt) outliers start: 16 outliers final: 16 residues processed: 139 average time/residue: 0.1752 time to fit residues: 34.4261 Evaluate side-chains 146 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 B residue 13 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 255 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 484 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 61 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.0010 chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3670 r_free = 0.3670 target = 0.136563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110347 restraints weight = 36051.152| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.72 r_work: 0.3199 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8698 Z= 0.158 Angle : 0.572 6.560 11751 Z= 0.280 Chirality : 0.036 0.141 1396 Planarity : 0.004 0.072 1457 Dihedral : 12.139 176.056 1318 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.07 % Allowed : 24.02 % Favored : 73.91 % 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 aren not related in a simple way. whole: 1.46 (0.27), residues: 1086 helix: 1.97 (0.19), residues: 798 sheet: -0.57 (0.66), residues: 60 loop : -2.33 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 439 TYR 0.012 0.002 TYR A 503 PHE 0.010 0.001 PHE B 328 TRP 0.011 0.001 TRP B 44 HIS 0.002 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8698) covalent geometry : angle 0.57240 (11751) hydrogen bonds : bond 0.04102 ( 572) hydrogen bonds : angle 3.87763 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.83 seconds wall clock time: 55 minutes 36.67 seconds (3336.67 seconds total)