Starting phenix.real_space_refine on Thu Jul 2 14:12:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8b_47715/07_2026/9e8b_47715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8b_47715/07_2026/9e8b_47715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e8b_47715/07_2026/9e8b_47715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8b_47715/07_2026/9e8b_47715.map" model { file = "/net/cci-nas-00/data/ceres_data/9e8b_47715/07_2026/9e8b_47715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8b_47715/07_2026/9e8b_47715.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 55 5.16 5 C 5371 2.51 5 N 1453 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8590 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4541 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 37, 'TRANS': 562} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3869 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 476} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 42 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 15 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8590 At special positions: 0 Unit cell: (70.62, 140.17, 105.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 55 16.00 Mg 1 11.99 O 1704 8.00 N 1453 7.00 C 5371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 461 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 486 " distance=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 497 " distance=2.16 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 497 " distance=2.14 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 527 " distance=2.05 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 532 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " BMA H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " NAG-ASN " NAG A 705 " - " ASN A 280 " " NAG B 604 " - " ASN B 125 " " NAG C 1 " - " ASN B 397 " " NAG E 1 " - " ASN B 346 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 513.1 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 18 sheets defined 15.5% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.732A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'B' and resid 28 through 34 removed outlier: 4.479A pdb=" N THR B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 33 " --> pdb=" O ASN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 removed outlier: 3.586A pdb=" N CYS B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.632A pdb=" N TRP B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 4.326A pdb=" N LYS B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.642A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.903A pdb=" N ALA B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.804A pdb=" N ARG B 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 288 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 329 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 365 through 379 Processing helix chain 'B' and resid 462 through 467 removed outlier: 4.029A pdb=" N GLN B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.537A pdb=" N THR A 40 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP A 465 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 455 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 451 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 58 removed outlier: 4.560A pdb=" N VAL A 84 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 273 Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 327 removed outlier: 3.568A pdb=" N LEU A 376 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 395 removed outlier: 6.400A pdb=" N ILE A 391 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA A 408 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA A 406 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 395 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 436 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 425 through 426 Processing sheet with id=AB2, first strand: chain 'A' and resid 552 through 554 removed outlier: 5.742A pdb=" N VAL A 485 " --> pdb=" O HIS A 618 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 563 through 566 Processing sheet with id=AB4, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AB5, first strand: chain 'B' and resid 86 through 91 removed outlier: 6.619A pdb=" N ARG B 113 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AB7, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AB8, first strand: chain 'B' and resid 216 through 223 removed outlier: 6.413A pdb=" N PHE B 179 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR B 221 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE B 177 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR B 223 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B 175 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 332 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY B 357 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE B 334 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 480 through 481 276 hydrogen bonds defined for protein. 726 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: 1.58 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2846 1.34 - 1.46: 1792 1.46 - 1.58: 4058 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 8768 Sorted by residual: bond pdb=" C PRO B 47 " pdb=" N MET B 48 " ideal model delta sigma weight residual 1.335 1.448 -0.112 1.34e-02 5.57e+03 7.05e+01 bond pdb=" C TYR A 197 " pdb=" N CYS A 198 " ideal model delta sigma weight residual 1.334 1.422 -0.088 1.27e-02 6.20e+03 4.76e+01 bond pdb=" C VAL A 616 " pdb=" N LEU A 617 " ideal model delta sigma weight residual 1.331 1.242 0.089 1.37e-02 5.33e+03 4.20e+01 bond pdb=" C THR B 33 " pdb=" N ARG B 34 " ideal model delta sigma weight residual 1.333 1.254 0.079 1.25e-02 6.40e+03 4.00e+01 bond pdb=" C LEU A 604 " pdb=" N PRO A 605 " ideal model delta sigma weight residual 1.335 1.264 0.070 1.15e-02 7.56e+03 3.72e+01 ... (remaining 8763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 11655 2.75 - 5.50: 259 5.50 - 8.25: 12 8.25 - 11.01: 1 11.01 - 13.76: 1 Bond angle restraints: 11928 Sorted by residual: angle pdb=" C LEU A 604 " pdb=" N PRO A 605 " pdb=" CA PRO A 605 " ideal model delta sigma weight residual 119.66 126.05 -6.39 7.20e-01 1.93e+00 7.87e+01 angle pdb=" O PRO B 47 " pdb=" C PRO B 47 " pdb=" N MET B 48 " ideal model delta sigma weight residual 122.23 130.24 -8.01 1.20e+00 6.94e-01 4.45e+01 angle pdb=" CA CYS B 527 " pdb=" CB CYS B 527 " pdb=" SG CYS B 527 " ideal model delta sigma weight residual 114.40 100.64 13.76 2.30e+00 1.89e-01 3.58e+01 angle pdb=" O VAL A 616 " pdb=" C VAL A 616 " pdb=" N LEU A 617 " ideal model delta sigma weight residual 122.99 117.09 5.90 1.07e+00 8.73e-01 3.04e+01 angle pdb=" O SER A 603 " pdb=" C SER A 603 " pdb=" N LEU A 604 " ideal model delta sigma weight residual 123.42 118.04 5.38 1.07e+00 8.73e-01 2.52e+01 ... (remaining 11923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 5117 21.32 - 42.65: 273 42.65 - 63.97: 46 63.97 - 85.29: 23 85.29 - 106.62: 14 Dihedral angle restraints: 5473 sinusoidal: 2315 harmonic: 3158 Sorted by residual: dihedral pdb=" CB CYS B 474 " pdb=" SG CYS B 474 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual 93.00 152.97 -59.97 1 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" CB CYS B 521 " pdb=" SG CYS B 521 " pdb=" SG CYS B 532 " pdb=" CB CYS B 532 " ideal model delta sinusoidal sigma weight residual -86.00 -140.88 54.88 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 497 " pdb=" CB CYS B 497 " ideal model delta sinusoidal sigma weight residual -86.00 -127.75 41.75 1 1.00e+01 1.00e-02 2.44e+01 ... (remaining 5470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1111 0.076 - 0.152: 212 0.152 - 0.227: 33 0.227 - 0.303: 4 0.303 - 0.379: 1 Chirality restraints: 1361 Sorted by residual: chirality pdb=" C1 NAG H 3 " pdb=" O4 NAG H 2 " pdb=" C2 NAG H 3 " pdb=" O5 NAG H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 9.91e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.18e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 BMA H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.87e+01 ... (remaining 1358 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.131 2.00e-02 2.50e+03 1.12e-01 1.57e+02 pdb=" C7 NAG H 2 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.026 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.184 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.104 2.00e-02 2.50e+03 8.57e-02 9.18e+01 pdb=" C7 NAG C 1 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.080 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.135 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 119 " 0.585 9.50e-02 1.11e+02 2.62e-01 4.20e+01 pdb=" NE ARG B 119 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG B 119 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 119 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 119 " 0.020 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 38 2.39 - 3.02: 5120 3.02 - 3.65: 13086 3.65 - 4.27: 20877 4.27 - 4.90: 34624 Nonbonded interactions: 73745 Sorted by model distance: nonbonded pdb=" OD1 ASP B 243 " pdb="CA CA B 602 " model vdw 1.763 3.250 nonbonded pdb=" OD1 ASP A 465 " pdb="CA CA A 704 " model vdw 2.169 3.250 nonbonded pdb=" OD1 ASP B 153 " pdb="CA CA B 603 " model vdw 2.184 3.250 nonbonded pdb=" OD1 ASP A 276 " pdb="CA CA A 702 " model vdw 2.187 3.250 nonbonded pdb=" OD1 ASN A 461 " pdb="CA CA A 704 " model vdw 2.187 3.250 ... (remaining 73740 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 'C' and resid 2) selection = (chain 'E' and resid 2) selection = (chain 'H' and resid 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.740 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 : 0.007 0.129 8797 Z= 0.507 Angle : 0.952 15.698 11996 Z= 0.596 Chirality : 0.061 0.379 1361 Planarity : 0.011 0.262 1562 Dihedral : 14.946 106.619 3398 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.63 % Favored : 94.19 % Rotamer: Outliers : 1.73 % Allowed : 12.66 % Favored : 85.61 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.25), residues: 1102 helix: -1.18 (0.44), residues: 122 sheet: -0.39 (0.27), residues: 357 loop : -0.90 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 430 TYR 0.010 0.001 TYR B 204 PHE 0.011 0.001 PHE B 481 TRP 0.013 0.001 TRP A 144 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.50 ( 8768) covalent geometry : angle 0.88669 / 0.58 (11928) SS BOND : bond 0.03859 / 2.36 ( 19) SS BOND : angle 3.65358 / 2.35 ( 38) hydrogen bonds : bond 0.22002 / 14.48 ( 272) hydrogen bonds : angle 9.89443 / 6.95 ( 726) link_BETA1-4 : bond 0.04519 / 2.43 ( 6) link_BETA1-4 : angle 6.95264 / 3.75 ( 18) link_NAG-ASN : bond 0.00443 / 0.22 ( 4) link_NAG-ASN : angle 3.05079 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 30 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8655 (pp) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 0.5392 time to fit residues: 36.1523 Evaluate side-chains 47 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.097168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.061317 restraints weight = 17778.423| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.75 r_work: 0.2777 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 8797 Z= 0.238 Angle : 0.679 9.180 11996 Z= 0.340 Chirality : 0.047 0.150 1361 Planarity : 0.004 0.035 1562 Dihedral : 9.847 70.600 1470 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.26 % Favored : 94.56 % Rotamer: Outliers : 2.71 % Allowed : 12.45 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1102 helix: -0.77 (0.46), residues: 122 sheet: -0.34 (0.27), residues: 345 loop : -0.80 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 242 TYR 0.013 0.001 TYR B 204 PHE 0.010 0.002 PHE A 222 TRP 0.013 0.001 TRP A 266 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 ( 8768) covalent geometry : angle 0.66103 / 0.33 (11928) SS BOND : bond 0.00913 / 0.44 ( 19) SS BOND : angle 1.65221 / 1.05 ( 38) hydrogen bonds : bond 0.04763 / 3.19 ( 272) hydrogen bonds : angle 7.28730 / 5.12 ( 726) link_BETA1-4 : bond 0.00738 / 0.39 ( 6) link_BETA1-4 : angle 2.97281 / 1.62 ( 18) link_NAG-ASN : bond 0.00210 / 0.11 ( 4) link_NAG-ASN : angle 2.00559 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.9167 (mtp85) cc_final: 0.8548 (ttm110) REVERT: B 48 MET cc_start: 0.8835 (pmm) cc_final: 0.8595 (pmm) REVERT: B 144 MET cc_start: 0.9350 (ttm) cc_final: 0.8966 (ttt) REVERT: B 213 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8631 (ttm) outliers start: 25 outliers final: 14 residues processed: 63 average time/residue: 0.4967 time to fit residues: 34.0611 Evaluate side-chains 50 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.095690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057032 restraints weight = 17116.821| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.82 r_work: 0.2753 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8797 Z= 0.164 Angle : 0.618 12.174 11996 Z= 0.308 Chirality : 0.046 0.157 1361 Planarity : 0.004 0.039 1562 Dihedral : 7.005 56.344 1464 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.90 % Favored : 94.92 % Rotamer: Outliers : 3.79 % Allowed : 12.23 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.25), residues: 1102 helix: -0.68 (0.45), residues: 124 sheet: -0.38 (0.27), residues: 341 loop : -0.77 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 487 TYR 0.011 0.001 TYR A 411 PHE 0.010 0.001 PHE A 222 TRP 0.012 0.001 TRP A 266 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 8768) covalent geometry : angle 0.59911 / 0.30 (11928) SS BOND : bond 0.00438 / 0.22 ( 19) SS BOND : angle 1.87406 / 1.17 ( 38) hydrogen bonds : bond 0.03799 / 2.54 ( 272) hydrogen bonds : angle 6.59223 / 4.61 ( 726) link_BETA1-4 : bond 0.00628 / 0.33 ( 6) link_BETA1-4 : angle 2.67080 / 1.44 ( 18) link_NAG-ASN : bond 0.00068 / 0.03 ( 4) link_NAG-ASN : angle 1.68207 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 42 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.9216 (mtp85) cc_final: 0.8974 (ttp80) REVERT: B 213 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8656 (ttm) REVERT: B 406 ILE cc_start: 0.8743 (pt) cc_final: 0.8440 (pp) REVERT: B 455 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.9004 (m) outliers start: 35 outliers final: 16 residues processed: 73 average time/residue: 0.4615 time to fit residues: 36.8835 Evaluate side-chains 55 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 0.0270 chunk 8 optimal weight: 0.0980 chunk 109 optimal weight: 40.0000 chunk 49 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3663 r_free = 0.3663 target = 0.097069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.059744 restraints weight = 17238.365| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.71 r_work: 0.2790 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8797 Z= 0.125 Angle : 0.587 11.198 11996 Z= 0.294 Chirality : 0.045 0.140 1361 Planarity : 0.004 0.046 1562 Dihedral : 5.438 56.768 1462 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.36 % Favored : 95.46 % Rotamer: Outliers : 3.03 % Allowed : 13.20 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.25), residues: 1102 helix: -0.48 (0.46), residues: 124 sheet: -0.32 (0.27), residues: 334 loop : -0.78 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 169 TYR 0.015 0.001 TYR B 204 PHE 0.009 0.001 PHE A 222 TRP 0.011 0.001 TRP A 266 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 8768) covalent geometry : angle 0.57136 / 0.29 (11928) SS BOND : bond 0.00486 / 0.25 ( 19) SS BOND : angle 1.68418 / 0.92 ( 38) hydrogen bonds : bond 0.03184 / 2.12 ( 272) hydrogen bonds : angle 6.22534 / 4.36 ( 726) link_BETA1-4 : bond 0.00593 / 0.31 ( 6) link_BETA1-4 : angle 2.39828 / 1.28 ( 18) link_NAG-ASN : bond 0.00113 / 0.06 ( 4) link_NAG-ASN : angle 1.57484 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 ARG cc_start: 0.9165 (mtp85) cc_final: 0.8614 (ttm110) REVERT: B 406 ILE cc_start: 0.8755 (pt) cc_final: 0.8423 (pp) REVERT: B 455 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.9076 (m) outliers start: 28 outliers final: 15 residues processed: 68 average time/residue: 0.4987 time to fit residues: 36.8866 Evaluate side-chains 53 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3695 r_free = 0.3695 target = 0.098838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062526 restraints weight = 17709.123| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.71 r_work: 0.2848 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8797 Z= 0.159 Angle : 0.599 13.775 11996 Z= 0.298 Chirality : 0.045 0.159 1361 Planarity : 0.004 0.048 1562 Dihedral : 5.063 59.576 1462 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.63 % Favored : 95.19 % Rotamer: Outliers : 3.25 % Allowed : 13.74 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1102 helix: -0.39 (0.47), residues: 124 sheet: -0.26 (0.27), residues: 349 loop : -0.81 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 543 TYR 0.011 0.001 TYR A 411 PHE 0.010 0.001 PHE B 274 TRP 0.011 0.001 TRP A 266 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 8768) covalent geometry : angle 0.58544 / 0.29 (11928) SS BOND : bond 0.00431 / 0.22 ( 19) SS BOND : angle 1.71403 / 0.85 ( 38) hydrogen bonds : bond 0.03123 / 2.10 ( 272) hydrogen bonds : angle 6.09007 / 4.26 ( 726) link_BETA1-4 : bond 0.00537 / 0.28 ( 6) link_BETA1-4 : angle 2.09427 / 1.12 ( 18) link_NAG-ASN : bond 0.00069 / 0.03 ( 4) link_NAG-ASN : angle 1.55581 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 38 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: B 144 MET cc_start: 0.9247 (ttm) cc_final: 0.8959 (ttt) REVERT: B 213 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8666 (ttm) REVERT: B 406 ILE cc_start: 0.8880 (pt) cc_final: 0.8545 (pp) REVERT: B 455 VAL cc_start: 0.9341 (OUTLIER) cc_final: 0.9123 (m) outliers start: 30 outliers final: 16 residues processed: 65 average time/residue: 0.4457 time to fit residues: 31.8583 Evaluate side-chains 52 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 109 optimal weight: 40.0000 chunk 62 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3682 r_free = 0.3682 target = 0.097975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.061625 restraints weight = 17553.432| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.69 r_work: 0.2824 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 8797 Z= 0.220 Angle : 0.631 15.564 11996 Z= 0.314 Chirality : 0.046 0.183 1361 Planarity : 0.004 0.046 1562 Dihedral : 4.981 58.857 1461 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.81 % Favored : 95.01 % Rotamer: Outliers : 3.35 % Allowed : 14.39 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.25), residues: 1102 helix: -0.45 (0.46), residues: 124 sheet: -0.30 (0.26), residues: 351 loop : -0.86 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 34 TYR 0.015 0.001 TYR B 204 PHE 0.011 0.001 PHE B 274 TRP 0.012 0.001 TRP A 266 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 8768) covalent geometry : angle 0.61808 / 0.31 (11928) SS BOND : bond 0.00566 / 0.30 ( 19) SS BOND : angle 1.82284 / 0.92 ( 38) hydrogen bonds : bond 0.03268 / 2.22 ( 272) hydrogen bonds : angle 6.07167 / 4.24 ( 726) link_BETA1-4 : bond 0.00465 / 0.24 ( 6) link_BETA1-4 : angle 1.92561 / 1.02 ( 18) link_NAG-ASN : bond 0.00192 / 0.10 ( 4) link_NAG-ASN : angle 1.59538 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 37 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8862 (mm) REVERT: B 213 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8690 (ttm) REVERT: B 406 ILE cc_start: 0.8912 (pt) cc_final: 0.8575 (pp) REVERT: B 455 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.9114 (m) outliers start: 31 outliers final: 17 residues processed: 64 average time/residue: 0.4067 time to fit residues: 28.7916 Evaluate side-chains 56 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3695 r_free = 0.3695 target = 0.098826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062439 restraints weight = 17720.750| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.71 r_work: 0.2848 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8797 Z= 0.154 Angle : 0.614 15.810 11996 Z= 0.305 Chirality : 0.046 0.227 1361 Planarity : 0.004 0.046 1562 Dihedral : 4.812 58.680 1460 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 2.71 % Allowed : 15.26 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1102 helix: -0.32 (0.47), residues: 124 sheet: -0.24 (0.26), residues: 349 loop : -0.83 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 34 TYR 0.011 0.001 TYR A 411 PHE 0.010 0.001 PHE B 274 TRP 0.012 0.001 TRP A 266 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 8768) covalent geometry : angle 0.60367 / 0.30 (11928) SS BOND : bond 0.00586 / 0.29 ( 19) SS BOND : angle 1.59136 / 0.79 ( 38) hydrogen bonds : bond 0.03088 / 2.07 ( 272) hydrogen bonds : angle 5.98935 / 4.18 ( 726) link_BETA1-4 : bond 0.00528 / 0.27 ( 6) link_BETA1-4 : angle 1.69550 / 0.91 ( 18) link_NAG-ASN : bond 0.00070 / 0.03 ( 4) link_NAG-ASN : angle 1.46230 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 39 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8907 (mm) REVERT: B 30 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8932 (tt) REVERT: B 213 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8650 (ttm) REVERT: B 406 ILE cc_start: 0.8916 (pt) cc_final: 0.8577 (pp) REVERT: B 455 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9107 (m) outliers start: 25 outliers final: 16 residues processed: 61 average time/residue: 0.4480 time to fit residues: 29.9527 Evaluate side-chains 57 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3693 r_free = 0.3693 target = 0.098753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062436 restraints weight = 17744.865| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.72 r_work: 0.2840 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8797 Z= 0.170 Angle : 0.621 15.125 11996 Z= 0.308 Chirality : 0.045 0.186 1361 Planarity : 0.004 0.046 1562 Dihedral : 4.741 57.493 1460 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 2.81 % Allowed : 15.80 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.25), residues: 1102 helix: -0.28 (0.47), residues: 124 sheet: -0.25 (0.27), residues: 350 loop : -0.85 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.014 0.001 TYR B 204 PHE 0.011 0.001 PHE B 274 TRP 0.012 0.001 TRP A 266 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 8768) covalent geometry : angle 0.61131 / 0.30 (11928) SS BOND : bond 0.00536 / 0.27 ( 19) SS BOND : angle 1.57985 / 0.78 ( 38) hydrogen bonds : bond 0.03092 / 2.07 ( 272) hydrogen bonds : angle 5.94254 / 4.14 ( 726) link_BETA1-4 : bond 0.00482 / 0.25 ( 6) link_BETA1-4 : angle 1.60555 / 0.86 ( 18) link_NAG-ASN : bond 0.00131 / 0.07 ( 4) link_NAG-ASN : angle 1.50178 / 0.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8922 (mm) REVERT: B 30 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8913 (tt) REVERT: B 213 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8649 (ttm) REVERT: B 406 ILE cc_start: 0.8957 (pt) cc_final: 0.8622 (pp) REVERT: B 455 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.9108 (m) outliers start: 26 outliers final: 17 residues processed: 62 average time/residue: 0.4502 time to fit residues: 30.6137 Evaluate side-chains 59 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 0.0670 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 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 = 0.3707 r_free = 0.3707 target = 0.099595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.063327 restraints weight = 17565.838| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.72 r_work: 0.2861 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8797 Z= 0.127 Angle : 0.617 15.579 11996 Z= 0.305 Chirality : 0.045 0.199 1361 Planarity : 0.004 0.048 1562 Dihedral : 4.641 57.013 1460 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 2.49 % Allowed : 16.23 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.25), residues: 1102 helix: -0.10 (0.48), residues: 124 sheet: -0.19 (0.27), residues: 350 loop : -0.85 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 169 TYR 0.011 0.001 TYR B 344 PHE 0.010 0.001 PHE B 274 TRP 0.012 0.001 TRP A 266 HIS 0.003 0.000 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8768) covalent geometry : angle 0.60935 / 0.30 (11928) SS BOND : bond 0.00550 / 0.27 ( 19) SS BOND : angle 1.40675 / 0.68 ( 38) hydrogen bonds : bond 0.02944 / 1.94 ( 272) hydrogen bonds : angle 5.79785 / 4.03 ( 726) link_BETA1-4 : bond 0.00510 / 0.26 ( 6) link_BETA1-4 : angle 1.43481 / 0.78 ( 18) link_NAG-ASN : bond 0.00104 / 0.05 ( 4) link_NAG-ASN : angle 1.39808 / 0.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8941 (mm) REVERT: B 30 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8919 (tt) REVERT: B 144 MET cc_start: 0.9209 (ttm) cc_final: 0.8976 (ttt) REVERT: B 455 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9102 (m) outliers start: 23 outliers final: 17 residues processed: 62 average time/residue: 0.4619 time to fit residues: 31.4421 Evaluate side-chains 57 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 0.4980 chunk 109 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.097627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061355 restraints weight = 17706.248| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.69 r_work: 0.2812 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 8797 Z= 0.257 Angle : 0.672 17.257 11996 Z= 0.334 Chirality : 0.047 0.220 1361 Planarity : 0.004 0.046 1562 Dihedral : 4.813 57.027 1460 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.54 % Favored : 94.37 % Rotamer: Outliers : 2.38 % Allowed : 16.23 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.25), residues: 1102 helix: -0.36 (0.47), residues: 124 sheet: -0.31 (0.26), residues: 351 loop : -0.87 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 430 TYR 0.013 0.002 TYR A 411 PHE 0.012 0.002 PHE B 274 TRP 0.010 0.002 TRP A 266 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.26 ( 8768) covalent geometry : angle 0.66188 / 0.33 (11928) SS BOND : bond 0.00632 / 0.32 ( 19) SS BOND : angle 1.70875 / 0.83 ( 38) hydrogen bonds : bond 0.03338 / 2.25 ( 272) hydrogen bonds : angle 5.97778 / 4.15 ( 726) link_BETA1-4 : bond 0.00485 / 0.25 ( 6) link_BETA1-4 : angle 1.58721 / 0.83 ( 18) link_NAG-ASN : bond 0.00299 / 0.15 ( 4) link_NAG-ASN : angle 1.61520 / 0.91 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8883 (mm) REVERT: B 30 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8925 (tt) REVERT: B 144 MET cc_start: 0.9278 (ttm) cc_final: 0.9006 (ttt) REVERT: B 150 MET cc_start: 0.9172 (mmm) cc_final: 0.8928 (mtp) REVERT: B 213 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8670 (ttm) REVERT: B 455 VAL cc_start: 0.9341 (OUTLIER) cc_final: 0.9122 (m) outliers start: 22 outliers final: 17 residues processed: 56 average time/residue: 0.4719 time to fit residues: 29.0480 Evaluate side-chains 57 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 527 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 0.0030 chunk 95 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.099463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063087 restraints weight = 17447.183| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.72 r_work: 0.2860 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8797 Z= 0.122 Angle : 0.619 15.418 11996 Z= 0.307 Chirality : 0.045 0.193 1361 Planarity : 0.004 0.048 1562 Dihedral : 4.642 56.998 1460 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 2.06 % Allowed : 16.67 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.25), residues: 1102 helix: -0.19 (0.48), residues: 126 sheet: -0.27 (0.27), residues: 345 loop : -0.83 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 430 TYR 0.010 0.001 TYR B 344 PHE 0.009 0.001 PHE A 222 TRP 0.013 0.001 TRP A 266 HIS 0.003 0.000 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 8768) covalent geometry : angle 0.61235 / 0.30 (11928) SS BOND : bond 0.00512 / 0.25 ( 19) SS BOND : angle 1.39811 / 0.68 ( 38) hydrogen bonds : bond 0.02915 / 1.94 ( 272) hydrogen bonds : angle 5.79779 / 4.03 ( 726) link_BETA1-4 : bond 0.00522 / 0.27 ( 6) link_BETA1-4 : angle 1.34308 / 0.74 ( 18) link_NAG-ASN : bond 0.00108 / 0.05 ( 4) link_NAG-ASN : angle 1.35774 / 0.77 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3369.82 seconds wall clock time: 58 minutes 18.00 seconds (3498.00 seconds total)