Starting phenix.real_space_refine on Sat Aug 23 04:13:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k17_36787/08_2025/8k17_36787.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k17_36787/08_2025/8k17_36787.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/8k17_36787/08_2025/8k17_36787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k17_36787/08_2025/8k17_36787.map" model { file = "/net/cci-nas-00/data/ceres_data/8k17_36787/08_2025/8k17_36787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k17_36787/08_2025/8k17_36787.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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 51 5.16 5 C 6207 2.51 5 N 1658 2.21 5 O 1831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 9748 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5193 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 33, 'TRANS': 612} Chain breaks: 2 Chain: "B" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2994 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "C" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1438 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 66 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 4, 'TRANS': 5} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' FE': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.69, per 1000 atoms: 0.17 Number of scatterers: 9748 At special positions: 0 Unit cell: (93.5, 115.5, 124.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 51 16.00 O 1831 8.00 N 1658 7.00 C 6207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 123 " distance=2.06 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 600 " distance=2.03 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 540 " " NAG A 802 " - " ASN A 316 " " NAG B 501 " - " ASN B 87 " " NAG B 502 " - " ASN B 363 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 268.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 57.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.798A pdb=" N LEU A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 83 removed outlier: 3.558A pdb=" N PHE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 125 removed outlier: 3.534A pdb=" N ALA A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.792A pdb=" N ASN A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.514A pdb=" N GLN A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 218 Processing helix chain 'A' and resid 220 through 223 Processing helix chain 'A' and resid 224 through 244 removed outlier: 3.510A pdb=" N ALA A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.654A pdb=" N THR A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.796A pdb=" N PHE A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.633A pdb=" N ASN A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 359 through 384 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.655A pdb=" N VAL A 398 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 428 Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.672A pdb=" N ARG A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 479 through 493 removed outlier: 3.661A pdb=" N CYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 528 Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.741A pdb=" N ALA A 535 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 699 removed outlier: 4.295A pdb=" N GLN A 689 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.533A pdb=" N GLU B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 41 " --> pdb=" O ARG B 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 37 through 41' Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 59 through 89 removed outlier: 3.558A pdb=" N SER B 63 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 88 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 89 " --> pdb=" O HIS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.625A pdb=" N GLN B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.520A pdb=" N ARG B 130 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN B 131 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 146 through 158 removed outlier: 4.204A pdb=" N PHE B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.932A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.933A pdb=" N LYS B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.641A pdb=" N SER B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 246 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.806A pdb=" N ASP B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 308 Processing helix chain 'B' and resid 310 through 325 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.551A pdb=" N HIS B 341 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.184A pdb=" N GLN B 353 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 379 removed outlier: 4.025A pdb=" N GLU B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.508A pdb=" N VAL C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 461 removed outlier: 5.798A pdb=" N LEU A 459 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP A 475 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A 676 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 613 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 674 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 615 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 672 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR A 617 " --> pdb=" O CYS A 670 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N CYS A 670 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR A 677 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N PHE A 561 " --> pdb=" O THR A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 592 through 594 removed outlier: 3.673A pdb=" N VAL A 601 " --> pdb=" O ILE A 592 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 623 through 624 removed outlier: 3.826A pdb=" N ARG A 666 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 641 removed outlier: 6.608A pdb=" N PHE A 629 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU A 640 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE A 627 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA6, first strand: chain 'B' and resid 384 through 386 removed outlier: 3.688A pdb=" N VAL C 12 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY C 26 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 20 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C 106 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP C 105 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 63 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 384 through 386 removed outlier: 8.062A pdb=" N GLY C 7 " --> pdb=" O PHE C 179 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N PHE C 179 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N LYS C 9 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 10.571A pdb=" N LYS C 177 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR C 11 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL C 175 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 169 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG C 19 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE C 167 " --> pdb=" O ARG C 19 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2783 1.33 - 1.45: 1797 1.45 - 1.57: 5330 1.57 - 1.69: 0 1.69 - 1.82: 77 Bond restraints: 9987 Sorted by residual: bond pdb=" CB CYS A 123 " pdb=" SG CYS A 123 " ideal model delta sigma weight residual 1.808 1.715 0.093 3.30e-02 9.18e+02 7.95e+00 bond pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " ideal model delta sigma weight residual 1.808 1.736 0.072 3.30e-02 9.18e+02 4.72e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C GLY A 254 " pdb=" O GLY A 254 " ideal model delta sigma weight residual 1.235 1.212 0.022 1.35e-02 5.49e+03 2.71e+00 bond pdb=" C TYR C 87 " pdb=" N GLY C 88 " ideal model delta sigma weight residual 1.331 1.307 0.023 1.46e-02 4.69e+03 2.54e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 13461 3.97 - 7.93: 39 7.93 - 11.90: 3 11.90 - 15.86: 0 15.86 - 19.83: 1 Bond angle restraints: 13504 Sorted by residual: angle pdb=" CA CYS A 123 " pdb=" CB CYS A 123 " pdb=" SG CYS A 123 " ideal model delta sigma weight residual 114.40 134.23 -19.83 2.30e+00 1.89e-01 7.43e+01 angle pdb=" C CYS A 123 " pdb=" CA CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sigma weight residual 110.42 99.27 11.15 1.99e+00 2.53e-01 3.14e+01 angle pdb=" C ARG A 122 " pdb=" N CYS A 123 " pdb=" CA CYS A 123 " ideal model delta sigma weight residual 121.54 111.78 9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" N CYS A 123 " pdb=" CA CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sigma weight residual 110.49 118.35 -7.86 1.69e+00 3.50e-01 2.16e+01 angle pdb=" C CYS A 75 " pdb=" N ARG A 76 " pdb=" CA ARG A 76 " ideal model delta sigma weight residual 120.28 114.96 5.32 1.34e+00 5.57e-01 1.58e+01 ... (remaining 13499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 5134 17.28 - 34.55: 670 34.55 - 51.83: 196 51.83 - 69.10: 40 69.10 - 86.38: 13 Dihedral angle restraints: 6053 sinusoidal: 2530 harmonic: 3523 Sorted by residual: dihedral pdb=" CA CYS A 123 " pdb=" C CYS A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta harmonic sigma weight residual 180.00 -139.93 -40.07 0 5.00e+00 4.00e-02 6.42e+01 dihedral pdb=" CA ARG A 122 " pdb=" C ARG A 122 " pdb=" N CYS A 123 " pdb=" CA CYS A 123 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LYS A 158 " pdb=" C LYS A 158 " pdb=" N LEU A 159 " pdb=" CA LEU A 159 " ideal model delta harmonic sigma weight residual 180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 6050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1202 0.067 - 0.133: 211 0.133 - 0.200: 10 0.200 - 0.267: 0 0.267 - 0.333: 1 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA CYS A 75 " pdb=" N CYS A 75 " pdb=" C CYS A 75 " pdb=" CB CYS A 75 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA PRO A 451 " pdb=" N PRO A 451 " pdb=" C PRO A 451 " pdb=" CB PRO A 451 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 1421 not shown) Planarity restraints: 1775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 603 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO A 604 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 621 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ASP A 621 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP A 621 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A 622 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 604 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 605 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " 0.029 5.00e-02 4.00e+02 ... (remaining 1772 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 43 2.56 - 3.15: 7435 3.15 - 3.73: 13829 3.73 - 4.32: 19123 4.32 - 4.90: 33240 Nonbonded interactions: 73670 Sorted by model distance: nonbonded pdb=" OD1 ASP A 589 " pdb="FE FE A 803 " model vdw 1.978 2.260 nonbonded pdb=" OG1 THR A 630 " pdb=" O THR A 636 " model vdw 2.085 3.040 nonbonded pdb=" N GLN B 27 " pdb=" NE2 GLN B 27 " model vdw 2.109 3.200 nonbonded pdb=" CE1 HIS A 659 " pdb="FE FE A 803 " model vdw 2.119 2.480 nonbonded pdb=" O ASP A 253 " pdb=" ND2 ASN A 256 " model vdw 2.135 3.120 ... (remaining 73665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.008 0.093 9993 Z= 0.329 Angle : 0.745 19.831 13520 Z= 0.397 Chirality : 0.049 0.333 1424 Planarity : 0.005 0.063 1771 Dihedral : 16.981 86.376 3787 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.29 % Allowed : 17.72 % Favored : 81.99 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.57 (0.24), residues: 1191 helix: 1.72 (0.20), residues: 633 sheet: 0.12 (0.48), residues: 105 loop : -1.57 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 74 TYR 0.021 0.002 TYR A 539 PHE 0.022 0.002 PHE B 324 TRP 0.010 0.002 TRP A 91 HIS 0.016 0.003 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00814 ( 9987) covalent geometry : angle 0.73681 (13504) SS BOND : bond 0.01702 ( 2) SS BOND : angle 6.04143 ( 4) hydrogen bonds : bond 0.18309 ( 522) hydrogen bonds : angle 5.48310 ( 1527) link_NAG-ASN : bond 0.00573 ( 4) link_NAG-ASN : angle 1.71544 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8671 (mmt) cc_final: 0.8114 (mmt) REVERT: B 341 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.7051 (m-70) outliers start: 3 outliers final: 0 residues processed: 115 average time/residue: 0.0710 time to fit residues: 11.9871 Evaluate side-chains 110 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118094 restraints weight = 11650.205| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.30 r_work: 0.3008 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9993 Z= 0.131 Angle : 0.500 6.840 13520 Z= 0.268 Chirality : 0.041 0.194 1424 Planarity : 0.004 0.050 1771 Dihedral : 4.428 40.980 1422 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.36 % Allowed : 18.40 % Favored : 80.23 % 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: 1.10 (0.24), residues: 1191 helix: 2.14 (0.21), residues: 635 sheet: 0.73 (0.50), residues: 94 loop : -1.38 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.015 0.001 TYR A 539 PHE 0.015 0.001 PHE B 156 TRP 0.012 0.001 TRP C 105 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9987) covalent geometry : angle 0.49482 (13504) SS BOND : bond 0.00600 ( 2) SS BOND : angle 2.76504 ( 4) hydrogen bonds : bond 0.06186 ( 522) hydrogen bonds : angle 3.91572 ( 1527) link_NAG-ASN : bond 0.00395 ( 4) link_NAG-ASN : angle 1.84388 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7584 (mm-30) REVERT: A 297 GLU cc_start: 0.7286 (pt0) cc_final: 0.7056 (mt-10) REVERT: A 337 MET cc_start: 0.8920 (tpp) cc_final: 0.8626 (tpt) REVERT: A 482 GLU cc_start: 0.7848 (mp0) cc_final: 0.7520 (mp0) REVERT: B 78 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7911 (mmt180) REVERT: C 67 ASP cc_start: 0.7270 (t0) cc_final: 0.6957 (t0) REVERT: C 154 LYS cc_start: 0.6819 (mtpt) cc_final: 0.6455 (ptmt) outliers start: 14 outliers final: 6 residues processed: 121 average time/residue: 0.0859 time to fit residues: 14.5215 Evaluate side-chains 115 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain C residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.151363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114811 restraints weight = 11705.979| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.59 r_work: 0.2863 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9993 Z= 0.148 Angle : 0.511 11.083 13520 Z= 0.271 Chirality : 0.040 0.159 1424 Planarity : 0.004 0.051 1771 Dihedral : 4.138 32.571 1420 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.63 % Allowed : 18.11 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.23 (0.24), residues: 1191 helix: 2.25 (0.21), residues: 637 sheet: 0.58 (0.50), residues: 100 loop : -1.29 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 569 TYR 0.016 0.001 TYR A 539 PHE 0.014 0.001 PHE C 121 TRP 0.008 0.001 TRP C 105 HIS 0.008 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9987) covalent geometry : angle 0.50271 (13504) SS BOND : bond 0.00260 ( 2) SS BOND : angle 4.71151 ( 4) hydrogen bonds : bond 0.06448 ( 522) hydrogen bonds : angle 3.75139 ( 1527) link_NAG-ASN : bond 0.00370 ( 4) link_NAG-ASN : angle 1.61391 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6060 (mm-30) REVERT: A 297 GLU cc_start: 0.7284 (pt0) cc_final: 0.7022 (mt-10) REVERT: A 337 MET cc_start: 0.8804 (tpp) cc_final: 0.8488 (tpt) REVERT: A 482 GLU cc_start: 0.7951 (mp0) cc_final: 0.7625 (mp0) REVERT: B 50 HIS cc_start: 0.7436 (m170) cc_final: 0.7175 (m170) REVERT: C 67 ASP cc_start: 0.7512 (t0) cc_final: 0.7201 (t0) REVERT: C 154 LYS cc_start: 0.6744 (mtpt) cc_final: 0.6425 (ptmt) outliers start: 27 outliers final: 11 residues processed: 133 average time/residue: 0.0822 time to fit residues: 15.4472 Evaluate side-chains 125 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115689 restraints weight = 11829.468| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.62 r_work: 0.2876 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9993 Z= 0.133 Angle : 0.477 6.727 13520 Z= 0.256 Chirality : 0.040 0.162 1424 Planarity : 0.004 0.050 1771 Dihedral : 3.883 25.896 1420 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.24 % Allowed : 18.31 % Favored : 79.45 % 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: 1.35 (0.24), residues: 1191 helix: 2.34 (0.20), residues: 637 sheet: 0.81 (0.50), residues: 94 loop : -1.26 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.015 0.001 TYR A 539 PHE 0.013 0.001 PHE C 121 TRP 0.008 0.001 TRP C 105 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9987) covalent geometry : angle 0.47078 (13504) SS BOND : bond 0.00518 ( 2) SS BOND : angle 3.58132 ( 4) hydrogen bonds : bond 0.05874 ( 522) hydrogen bonds : angle 3.64509 ( 1527) link_NAG-ASN : bond 0.00344 ( 4) link_NAG-ASN : angle 1.56148 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8126 (m-30) cc_final: 0.7908 (m-30) REVERT: A 134 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6116 (mm-30) REVERT: A 297 GLU cc_start: 0.7263 (pt0) cc_final: 0.7014 (mt-10) REVERT: A 337 MET cc_start: 0.8818 (tpp) cc_final: 0.8471 (tpt) REVERT: A 482 GLU cc_start: 0.7957 (mp0) cc_final: 0.7619 (mp0) REVERT: B 27 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: B 50 HIS cc_start: 0.7453 (m170) cc_final: 0.7181 (m170) REVERT: C 67 ASP cc_start: 0.7650 (t0) cc_final: 0.7296 (t0) REVERT: C 154 LYS cc_start: 0.6754 (mtpt) cc_final: 0.6444 (ptmt) outliers start: 23 outliers final: 13 residues processed: 129 average time/residue: 0.0761 time to fit residues: 14.1735 Evaluate side-chains 131 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.155006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.119030 restraints weight = 11620.940| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.23 r_work: 0.2890 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9993 Z= 0.146 Angle : 0.505 10.820 13520 Z= 0.266 Chirality : 0.040 0.165 1424 Planarity : 0.004 0.050 1771 Dihedral : 3.803 21.572 1420 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.02 % Allowed : 18.21 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.24), residues: 1191 helix: 2.37 (0.20), residues: 637 sheet: 0.79 (0.50), residues: 94 loop : -1.27 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.015 0.001 TYR A 539 PHE 0.014 0.001 PHE C 121 TRP 0.007 0.001 TRP C 105 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9987) covalent geometry : angle 0.49340 (13504) SS BOND : bond 0.00262 ( 2) SS BOND : angle 5.72142 ( 4) hydrogen bonds : bond 0.06172 ( 522) hydrogen bonds : angle 3.65804 ( 1527) link_NAG-ASN : bond 0.00346 ( 4) link_NAG-ASN : angle 1.55528 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6105 (mm-30) REVERT: A 337 MET cc_start: 0.8803 (tpp) cc_final: 0.8402 (tpt) REVERT: A 482 GLU cc_start: 0.7937 (mp0) cc_final: 0.7592 (mp0) REVERT: B 50 HIS cc_start: 0.7425 (m170) cc_final: 0.7148 (m170) REVERT: B 282 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8903 (t) REVERT: C 67 ASP cc_start: 0.7627 (t0) cc_final: 0.7275 (t0) REVERT: C 154 LYS cc_start: 0.6900 (mtpt) cc_final: 0.6608 (ptmt) outliers start: 31 outliers final: 16 residues processed: 141 average time/residue: 0.0741 time to fit residues: 15.1288 Evaluate side-chains 133 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.156305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121345 restraints weight = 11667.494| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.31 r_work: 0.2947 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9993 Z= 0.110 Angle : 0.470 10.033 13520 Z= 0.249 Chirality : 0.039 0.177 1424 Planarity : 0.004 0.048 1771 Dihedral : 3.570 21.068 1420 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.85 % Allowed : 19.86 % Favored : 78.29 % 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: 1.52 (0.24), residues: 1191 helix: 2.49 (0.20), residues: 637 sheet: 0.86 (0.51), residues: 96 loop : -1.19 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.014 0.001 TYR A 539 PHE 0.010 0.001 PHE C 121 TRP 0.009 0.001 TRP C 105 HIS 0.003 0.000 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9987) covalent geometry : angle 0.45952 (13504) SS BOND : bond 0.00209 ( 2) SS BOND : angle 5.23757 ( 4) hydrogen bonds : bond 0.05057 ( 522) hydrogen bonds : angle 3.50520 ( 1527) link_NAG-ASN : bond 0.00312 ( 4) link_NAG-ASN : angle 1.53609 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7968 (m-30) cc_final: 0.7692 (m-30) REVERT: A 134 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5918 (mm-30) REVERT: A 259 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: A 337 MET cc_start: 0.8744 (tpp) cc_final: 0.8285 (tpt) REVERT: A 448 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 482 GLU cc_start: 0.7904 (mp0) cc_final: 0.7579 (mp0) REVERT: B 50 HIS cc_start: 0.7273 (m170) cc_final: 0.6977 (m170) REVERT: B 282 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8820 (t) REVERT: C 67 ASP cc_start: 0.7592 (t0) cc_final: 0.7228 (t0) REVERT: C 154 LYS cc_start: 0.6876 (mtpt) cc_final: 0.6558 (ptmt) outliers start: 19 outliers final: 11 residues processed: 133 average time/residue: 0.0762 time to fit residues: 14.5636 Evaluate side-chains 125 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.149662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109901 restraints weight = 11732.656| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.64 r_work: 0.2877 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9993 Z= 0.111 Angle : 0.466 7.883 13520 Z= 0.244 Chirality : 0.039 0.167 1424 Planarity : 0.004 0.047 1771 Dihedral : 3.500 19.291 1420 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.43 % Allowed : 19.47 % Favored : 78.09 % 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: 1.56 (0.24), residues: 1191 helix: 2.52 (0.20), residues: 637 sheet: 0.88 (0.51), residues: 96 loop : -1.18 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.014 0.001 TYR A 539 PHE 0.011 0.001 PHE C 121 TRP 0.008 0.001 TRP C 105 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9987) covalent geometry : angle 0.45833 (13504) SS BOND : bond 0.00395 ( 2) SS BOND : angle 4.15582 ( 4) hydrogen bonds : bond 0.05109 ( 522) hydrogen bonds : angle 3.47115 ( 1527) link_NAG-ASN : bond 0.00315 ( 4) link_NAG-ASN : angle 1.50239 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.305 Fit side-chains REVERT: A 78 GLN cc_start: 0.7795 (tt0) cc_final: 0.7508 (tt0) REVERT: A 106 ASP cc_start: 0.7917 (m-30) cc_final: 0.7649 (m-30) REVERT: A 134 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.6140 (mm-30) REVERT: A 259 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: A 482 GLU cc_start: 0.7867 (mp0) cc_final: 0.7586 (mp0) REVERT: B 50 HIS cc_start: 0.7487 (m170) cc_final: 0.7189 (m170) REVERT: B 282 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8942 (t) REVERT: C 154 LYS cc_start: 0.6863 (mtpt) cc_final: 0.6571 (ptmt) outliers start: 25 outliers final: 15 residues processed: 134 average time/residue: 0.0771 time to fit residues: 14.9598 Evaluate side-chains 131 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 HIS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 101 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.153627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.118311 restraints weight = 11631.694| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.31 r_work: 0.2884 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9993 Z= 0.178 Angle : 0.537 10.329 13520 Z= 0.285 Chirality : 0.042 0.253 1424 Planarity : 0.004 0.049 1771 Dihedral : 3.755 23.790 1420 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.73 % Allowed : 18.79 % Favored : 78.48 % 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: 1.39 (0.24), residues: 1191 helix: 2.39 (0.20), residues: 638 sheet: 0.48 (0.50), residues: 103 loop : -1.21 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 687 TYR 0.016 0.001 TYR A 539 PHE 0.017 0.002 PHE C 121 TRP 0.006 0.001 TRP C 105 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9987) covalent geometry : angle 0.53065 (13504) SS BOND : bond 0.00473 ( 2) SS BOND : angle 4.11409 ( 4) hydrogen bonds : bond 0.06800 ( 522) hydrogen bonds : angle 3.69292 ( 1527) link_NAG-ASN : bond 0.00340 ( 4) link_NAG-ASN : angle 1.55315 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.351 Fit side-chains REVERT: A 78 GLN cc_start: 0.7681 (tt0) cc_final: 0.7328 (tt0) REVERT: A 134 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6204 (mm-30) REVERT: A 259 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: A 482 GLU cc_start: 0.7918 (mp0) cc_final: 0.7561 (mp0) REVERT: B 50 HIS cc_start: 0.7346 (m170) cc_final: 0.7050 (m170) REVERT: B 282 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8941 (t) REVERT: C 154 LYS cc_start: 0.6816 (mtpt) cc_final: 0.6523 (ptmt) outliers start: 28 outliers final: 20 residues processed: 129 average time/residue: 0.0824 time to fit residues: 15.4837 Evaluate side-chains 133 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 74 optimal weight: 0.0040 chunk 109 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 99 optimal weight: 0.0170 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.151064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110979 restraints weight = 11711.324| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.68 r_work: 0.2904 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9993 Z= 0.102 Angle : 0.474 9.035 13520 Z= 0.249 Chirality : 0.039 0.194 1424 Planarity : 0.004 0.048 1771 Dihedral : 3.487 22.862 1420 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.66 % Allowed : 20.06 % Favored : 78.29 % 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: 1.57 (0.24), residues: 1191 helix: 2.52 (0.20), residues: 637 sheet: 0.84 (0.51), residues: 96 loop : -1.15 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.011 0.001 TYR A 539 PHE 0.009 0.001 PHE C 121 TRP 0.010 0.001 TRP C 105 HIS 0.002 0.000 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 9987) covalent geometry : angle 0.46666 (13504) SS BOND : bond 0.00558 ( 2) SS BOND : angle 3.99376 ( 4) hydrogen bonds : bond 0.04580 ( 522) hydrogen bonds : angle 3.44234 ( 1527) link_NAG-ASN : bond 0.00280 ( 4) link_NAG-ASN : angle 1.55911 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.383 Fit side-chains REVERT: A 78 GLN cc_start: 0.7770 (tt0) cc_final: 0.7457 (tt0) REVERT: A 106 ASP cc_start: 0.7888 (m-30) cc_final: 0.7623 (m-30) REVERT: A 259 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: A 448 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 482 GLU cc_start: 0.7837 (mp0) cc_final: 0.7558 (mp0) REVERT: B 50 HIS cc_start: 0.7440 (m170) cc_final: 0.7138 (m170) REVERT: B 282 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.9001 (t) REVERT: C 154 LYS cc_start: 0.6896 (mtpt) cc_final: 0.6593 (ptmt) outliers start: 17 outliers final: 12 residues processed: 129 average time/residue: 0.0823 time to fit residues: 15.1743 Evaluate side-chains 124 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121381 restraints weight = 11525.712| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.36 r_work: 0.3022 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9993 Z= 0.111 Angle : 0.477 8.754 13520 Z= 0.251 Chirality : 0.039 0.206 1424 Planarity : 0.004 0.047 1771 Dihedral : 3.440 22.688 1420 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.17 % Allowed : 20.16 % Favored : 78.68 % 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: 1.66 (0.24), residues: 1191 helix: 2.59 (0.20), residues: 637 sheet: 0.92 (0.51), residues: 95 loop : -1.10 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 183 TYR 0.013 0.001 TYR A 539 PHE 0.011 0.001 PHE C 121 TRP 0.009 0.001 TRP C 105 HIS 0.003 0.000 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9987) covalent geometry : angle 0.47063 (13504) SS BOND : bond 0.00454 ( 2) SS BOND : angle 3.75506 ( 4) hydrogen bonds : bond 0.04924 ( 522) hydrogen bonds : angle 3.42791 ( 1527) link_NAG-ASN : bond 0.00300 ( 4) link_NAG-ASN : angle 1.46850 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.323 Fit side-chains REVERT: A 78 GLN cc_start: 0.7788 (tt0) cc_final: 0.7465 (tt0) REVERT: A 106 ASP cc_start: 0.8109 (m-30) cc_final: 0.7836 (m-30) REVERT: A 259 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: A 448 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7767 (mm-30) REVERT: A 482 GLU cc_start: 0.7891 (mp0) cc_final: 0.7558 (mp0) REVERT: B 50 HIS cc_start: 0.7469 (m170) cc_final: 0.7161 (m170) REVERT: B 282 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9022 (t) REVERT: C 154 LYS cc_start: 0.6922 (mtpt) cc_final: 0.6608 (ptmt) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 0.0830 time to fit residues: 14.9271 Evaluate side-chains 127 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 101 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.155136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120283 restraints weight = 11635.708| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.32 r_work: 0.2930 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9993 Z= 0.116 Angle : 0.485 8.632 13520 Z= 0.254 Chirality : 0.039 0.203 1424 Planarity : 0.004 0.047 1771 Dihedral : 3.429 22.430 1420 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.46 % Allowed : 20.16 % Favored : 78.38 % 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: 1.65 (0.24), residues: 1191 helix: 2.54 (0.20), residues: 643 sheet: 0.97 (0.51), residues: 95 loop : -1.09 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 183 TYR 0.014 0.001 TYR A 539 PHE 0.011 0.001 PHE C 91 TRP 0.007 0.001 TRP C 105 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9987) covalent geometry : angle 0.47855 (13504) SS BOND : bond 0.00414 ( 2) SS BOND : angle 3.73857 ( 4) hydrogen bonds : bond 0.05153 ( 522) hydrogen bonds : angle 3.43581 ( 1527) link_NAG-ASN : bond 0.00284 ( 4) link_NAG-ASN : angle 1.46018 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.81 seconds wall clock time: 38 minutes 49.87 seconds (2329.87 seconds total)