Starting phenix.real_space_refine on Mon Jun 16 01:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8by2_16319/06_2025/8by2_16319_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8by2_16319/06_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_16319/06_2025/8by2_16319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8by2_16319/06_2025/8by2_16319.map" model { file = "/net/cci-nas-00/data/ceres_data/8by2_16319/06_2025/8by2_16319_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8by2_16319/06_2025/8by2_16319_trim.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.09, per 1000 atoms: 0.52 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: 4.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.25 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: 5.88 Time building geometry restraints manager: 5.82 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 560 or resid 601 throug \ h 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 560 or resid 601 t \ hrough 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: 50.320 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: 0.280 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 38.600 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 44 HIS 0.003 0.001 HIS B 259 PHE 0.008 0.001 PHE A 410 TYR 0.019 0.001 TYR A 538 ARG 0.002 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.06895 ( 572) hydrogen bonds : angle 4.08771 ( 1701) covalent geometry : bond 0.00281 ( 8698) covalent geometry : angle 0.58130 (11751) *********************** 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 : 1.355 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.4465 time to fit residues: 86.1234 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 : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.138809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111460 restraints weight = 35390.497| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.79 r_work: 0.3198 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0472 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= 0.172 Angle : 0.557 6.455 11751 Z= 0.275 Chirality : 0.036 0.148 1396 Planarity : 0.004 0.058 1457 Dihedral : 14.547 175.467 1318 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.49 % Allowed : 24.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1086 helix: 2.05 (0.19), residues: 800 sheet: -0.62 (0.64), residues: 60 loop : -2.36 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.003 0.001 HIS B 259 PHE 0.010 0.001 PHE A 410 TYR 0.016 0.002 TYR B 257 ARG 0.002 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 572) hydrogen bonds : angle 3.83784 ( 1701) covalent geometry : bond 0.00386 ( 8698) covalent geometry : angle 0.55651 (11751) *********************** 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 146 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 140 average time/residue: 0.6953 time to fit residues: 136.4484 Evaluate side-chains 139 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 2.002 ------------------------------------------------------------------------------- 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 348 MET 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 100 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.141094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113795 restraints weight = 35221.944| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.80 r_work: 0.3243 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0484 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= 0.102 Angle : 0.518 5.951 11751 Z= 0.250 Chirality : 0.034 0.144 1396 Planarity : 0.004 0.054 1457 Dihedral : 14.029 174.680 1318 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.26 % Allowed : 24.02 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 1086 helix: 2.18 (0.19), residues: 800 sheet: -0.69 (0.63), residues: 60 loop : -2.25 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 PHE 0.009 0.001 PHE A 410 TYR 0.008 0.001 TYR B 503 ARG 0.005 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 572) hydrogen bonds : angle 3.67960 ( 1701) covalent geometry : bond 0.00226 ( 8698) covalent geometry : angle 0.51813 (11751) *********************** 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 150 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 3.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 MET cc_start: 0.7920 (tpp) cc_final: 0.7606 (mmt) outliers start: 11 outliers final: 10 residues processed: 144 average time/residue: 0.7053 time to fit residues: 149.9424 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 : 3.224 ------------------------------------------------------------------------------- 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 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 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 17 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.139052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111703 restraints weight = 35567.657| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.81 r_work: 0.3203 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0649 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 : 0.540 6.218 11751 Z= 0.263 Chirality : 0.035 0.141 1396 Planarity : 0.004 0.053 1457 Dihedral : 13.809 175.114 1318 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 1086 helix: 2.07 (0.19), residues: 800 sheet: -0.68 (0.64), residues: 60 loop : -2.32 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 PHE 0.009 0.001 PHE B 328 TYR 0.012 0.001 TYR B 538 ARG 0.008 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 572) hydrogen bonds : angle 3.77840 ( 1701) covalent geometry : bond 0.00320 ( 8698) covalent geometry : angle 0.54002 (11751) *********************** 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 152 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 146 average time/residue: 0.5276 time to fit residues: 107.2326 Evaluate side-chains 143 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 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 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 55 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.136882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110309 restraints weight = 35882.148| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.78 r_work: 0.3190 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0765 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= 0.151 Angle : 0.554 6.367 11751 Z= 0.271 Chirality : 0.036 0.142 1396 Planarity : 0.004 0.052 1457 Dihedral : 13.463 175.498 1318 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.07 % Allowed : 22.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 1086 helix: 1.98 (0.19), residues: 800 sheet: -0.67 (0.64), residues: 60 loop : -2.37 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 PHE 0.010 0.001 PHE B 328 TYR 0.016 0.002 TYR B 538 ARG 0.010 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 572) hydrogen bonds : angle 3.84594 ( 1701) covalent geometry : bond 0.00341 ( 8698) covalent geometry : angle 0.55432 (11751) *********************** 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 151 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.4716 (OUTLIER) cc_final: 0.3895 (mt) outliers start: 18 outliers final: 16 residues processed: 144 average time/residue: 0.6588 time to fit residues: 138.5444 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 : 1.358 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.137237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109907 restraints weight = 35534.490| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.80 r_work: 0.3177 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0922 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= 0.166 Angle : 0.563 6.533 11751 Z= 0.278 Chirality : 0.036 0.142 1396 Planarity : 0.004 0.053 1457 Dihedral : 13.130 175.886 1318 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.30 % Allowed : 22.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.27), residues: 1086 helix: 1.87 (0.19), residues: 805 sheet: -0.73 (0.64), residues: 60 loop : -2.57 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.003 0.001 HIS B 434 PHE 0.010 0.001 PHE B 328 TYR 0.017 0.002 TYR B 538 ARG 0.007 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 572) hydrogen bonds : angle 3.92014 ( 1701) covalent geometry : bond 0.00377 ( 8698) covalent geometry : angle 0.56343 (11751) *********************** 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 152 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.4584 (OUTLIER) cc_final: 0.3699 (mt) outliers start: 20 outliers final: 17 residues processed: 143 average time/residue: 0.4376 time to fit residues: 87.4526 Evaluate side-chains 149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 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 367 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.137053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109767 restraints weight = 35545.591| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.79 r_work: 0.3175 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0993 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= 0.162 Angle : 0.568 6.561 11751 Z= 0.280 Chirality : 0.036 0.144 1396 Planarity : 0.004 0.058 1457 Dihedral : 12.879 175.768 1318 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.18 % Allowed : 22.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1086 helix: 1.86 (0.19), residues: 799 sheet: -0.67 (0.65), residues: 60 loop : -2.50 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 PHE 0.010 0.001 PHE B 328 TYR 0.014 0.002 TYR B 538 ARG 0.009 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 572) hydrogen bonds : angle 3.93924 ( 1701) covalent geometry : bond 0.00369 ( 8698) covalent geometry : angle 0.56782 (11751) *********************** 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 154 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.4660 (OUTLIER) cc_final: 0.3762 (mt) outliers start: 19 outliers final: 15 residues processed: 147 average time/residue: 0.5281 time to fit residues: 107.2059 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 : 2.155 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE 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 348 MET Chi-restraints excluded: chain B residue 367 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.138340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111565 restraints weight = 35233.473| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.76 r_work: 0.3211 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8698 Z= 0.111 Angle : 0.549 6.358 11751 Z= 0.266 Chirality : 0.035 0.155 1396 Planarity : 0.004 0.062 1457 Dihedral : 12.465 174.646 1318 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.07 % Allowed : 23.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.27), residues: 1086 helix: 1.94 (0.19), residues: 805 sheet: -0.62 (0.65), residues: 60 loop : -2.49 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 PHE 0.009 0.001 PHE A 410 TYR 0.022 0.002 TYR B 538 ARG 0.009 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 572) hydrogen bonds : angle 3.81673 ( 1701) covalent geometry : bond 0.00244 ( 8698) covalent geometry : angle 0.54888 (11751) *********************** 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: 18 poor density : 132 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.4552 (OUTLIER) cc_final: 0.3671 (mt) outliers start: 18 outliers final: 15 residues processed: 143 average time/residue: 0.4534 time to fit residues: 90.7229 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 : 1.399 ------------------------------------------------------------------------------- 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 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 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 255 SER Chi-restraints excluded: chain B residue 367 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112754 restraints weight = 35723.558| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.71 r_work: 0.3230 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0971 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= 0.108 Angle : 0.541 6.312 11751 Z= 0.261 Chirality : 0.035 0.143 1396 Planarity : 0.004 0.066 1457 Dihedral : 12.162 174.339 1318 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.72 % Allowed : 23.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.27), residues: 1086 helix: 2.06 (0.19), residues: 799 sheet: -0.60 (0.65), residues: 60 loop : -2.39 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 PHE 0.008 0.001 PHE A 410 TYR 0.017 0.001 TYR B 538 ARG 0.010 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 572) hydrogen bonds : angle 3.75836 ( 1701) covalent geometry : bond 0.00238 ( 8698) covalent geometry : angle 0.54113 (11751) *********************** 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: 15 poor density : 133 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 143 average time/residue: 0.4466 time to fit residues: 90.2613 Evaluate side-chains 146 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER 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 367 SER Chi-restraints excluded: chain B residue 496 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113369 restraints weight = 35371.530| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.69 r_work: 0.3241 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0985 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= 0.102 Angle : 0.542 6.929 11751 Z= 0.260 Chirality : 0.035 0.143 1396 Planarity : 0.004 0.069 1457 Dihedral : 12.038 174.248 1318 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.72 % Allowed : 23.56 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 1086 helix: 2.06 (0.19), residues: 805 sheet: -0.56 (0.65), residues: 60 loop : -2.44 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 PHE 0.008 0.001 PHE A 410 TYR 0.016 0.001 TYR B 538 ARG 0.012 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 572) hydrogen bonds : angle 3.72648 ( 1701) covalent geometry : bond 0.00225 ( 8698) covalent geometry : angle 0.54192 (11751) ********************** 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: 15 poor density : 134 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 144 average time/residue: 0.4279 time to fit residues: 86.9487 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 : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER 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 367 SER 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 65 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.138457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111512 restraints weight = 35642.217| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.76 r_work: 0.3202 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1031 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= 0.136 Angle : 0.559 6.519 11751 Z= 0.270 Chirality : 0.035 0.141 1396 Planarity : 0.004 0.070 1457 Dihedral : 12.067 175.102 1318 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.95 % Allowed : 23.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 1086 helix: 2.01 (0.19), residues: 799 sheet: -0.54 (0.66), residues: 60 loop : -2.41 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 PHE 0.009 0.001 PHE A 410 TYR 0.015 0.002 TYR B 538 ARG 0.013 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 572) hydrogen bonds : angle 3.81116 ( 1701) covalent geometry : bond 0.00309 ( 8698) covalent geometry : angle 0.55883 (11751) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8543.91 seconds wall clock time: 151 minutes 5.41 seconds (9065.41 seconds total)