Starting phenix.real_space_refine on Wed Feb 4 04:46:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8b_47715/02_2026/9e8b_47715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8b_47715/02_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_47715/02_2026/9e8b_47715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8b_47715/02_2026/9e8b_47715.map" model { file = "/net/cci-nas-00/data/ceres_data/9e8b_47715/02_2026/9e8b_47715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8b_47715/02_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-2.0-5952/lib/python3.9/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, 46 Unusual residues: {' CA': 4, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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, 17 Unusual residues: {' CA': 2, ' MG': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.16, per 1000 atoms: 0.25 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: 0.82 Conformation dependent library (CDL) restraints added in 333.1 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: 0.35 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: 1.60 Time building geometry restraints manager: 1.03 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 2.510 nonbonded pdb=" OD1 ASP A 465 " pdb="CA CA A 704 " model vdw 2.169 2.510 nonbonded pdb=" OD1 ASP B 153 " pdb="CA CA B 603 " model vdw 2.184 2.510 nonbonded pdb=" OD1 ASP A 276 " pdb="CA CA A 702 " model vdw 2.187 2.510 nonbonded pdb=" OD1 ASN A 461 " pdb="CA CA A 704 " model vdw 2.187 2.510 ... (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: 1.810 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.020 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 covalent geometry : bond 0.00717 ( 8768) covalent geometry : angle 0.88669 (11928) SS BOND : bond 0.03859 ( 19) SS BOND : angle 3.65358 ( 38) hydrogen bonds : bond 0.22002 ( 272) hydrogen bonds : angle 9.89443 ( 726) link_BETA1-4 : bond 0.04519 ( 6) link_BETA1-4 : angle 6.95264 ( 18) link_NAG-ASN : bond 0.00443 ( 4) link_NAG-ASN : angle 3.05079 ( 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 : 0.204 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: 0.5317 time to fit residues: 35.4710 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 : 0.335 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3641 r_free = 0.3641 target = 0.096667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.060826 restraints weight = 17793.400| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.74 r_work: 0.2777 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8797 Z= 0.233 Angle : 0.673 9.153 11996 Z= 0.336 Chirality : 0.047 0.149 1361 Planarity : 0.004 0.035 1562 Dihedral : 9.787 70.400 1470 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.17 % Favored : 94.65 % Rotamer: Outliers : 2.81 % Allowed : 12.23 % Favored : 84.96 % 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: -1.00 (0.25), residues: 1102 helix: -0.81 (0.45), residues: 122 sheet: -0.33 (0.27), residues: 345 loop : -0.77 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 242 TYR 0.013 0.001 TYR B 204 PHE 0.011 0.002 PHE A 162 TRP 0.013 0.001 TRP A 266 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 8768) covalent geometry : angle 0.65510 (11928) SS BOND : bond 0.00313 ( 19) SS BOND : angle 1.71074 ( 38) hydrogen bonds : bond 0.04465 ( 272) hydrogen bonds : angle 7.25558 ( 726) link_BETA1-4 : bond 0.00654 ( 6) link_BETA1-4 : angle 2.95471 ( 18) link_NAG-ASN : bond 0.00180 ( 4) link_NAG-ASN : angle 1.99374 ( 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 70 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.9185 (mtp85) cc_final: 0.8583 (ttm110) REVERT: B 48 MET cc_start: 0.8852 (pmm) cc_final: 0.8610 (pmm) REVERT: B 144 MET cc_start: 0.9343 (ttm) cc_final: 0.8961 (ttt) REVERT: B 213 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8684 (ttm) outliers start: 26 outliers final: 13 residues processed: 65 average time/residue: 0.4909 time to fit residues: 34.8272 Evaluate side-chains 49 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3597 r_free = 0.3597 target = 0.094277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055756 restraints weight = 17232.540| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.79 r_work: 0.2719 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 8797 Z= 0.193 Angle : 0.626 11.857 11996 Z= 0.312 Chirality : 0.046 0.156 1361 Planarity : 0.004 0.033 1562 Dihedral : 7.081 56.362 1464 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.90 % Favored : 94.92 % Rotamer: Outliers : 3.68 % Allowed : 12.45 % Favored : 83.87 % 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: -1.00 (0.25), residues: 1102 helix: -0.77 (0.45), residues: 124 sheet: -0.37 (0.27), residues: 346 loop : -0.75 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 242 TYR 0.012 0.001 TYR A 411 PHE 0.010 0.001 PHE B 274 TRP 0.013 0.001 TRP A 266 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 8768) covalent geometry : angle 0.60743 (11928) SS BOND : bond 0.00436 ( 19) SS BOND : angle 1.89182 ( 38) hydrogen bonds : bond 0.03838 ( 272) hydrogen bonds : angle 6.64374 ( 726) link_BETA1-4 : bond 0.00623 ( 6) link_BETA1-4 : angle 2.71443 ( 18) link_NAG-ASN : bond 0.00080 ( 4) link_NAG-ASN : angle 1.72478 ( 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 75 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 41 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: B 34 ARG cc_start: 0.9226 (mtp85) cc_final: 0.8971 (ttp80) REVERT: B 191 MET cc_start: 0.9406 (ttp) cc_final: 0.9191 (ttp) REVERT: B 213 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8693 (ttm) REVERT: B 406 ILE cc_start: 0.8712 (pt) cc_final: 0.8391 (pp) REVERT: B 435 GLU cc_start: 0.8675 (mp0) cc_final: 0.8322 (mp0) REVERT: B 455 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9033 (m) outliers start: 34 outliers final: 17 residues processed: 72 average time/residue: 0.4606 time to fit residues: 36.2622 Evaluate side-chains 56 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 0.0060 chunk 8 optimal weight: 0.9990 chunk 109 optimal weight: 50.0000 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3638 r_free = 0.3638 target = 0.095830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.057919 restraints weight = 17417.278| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.75 r_work: 0.2748 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8797 Z= 0.138 Angle : 0.586 11.417 11996 Z= 0.293 Chirality : 0.044 0.147 1361 Planarity : 0.004 0.045 1562 Dihedral : 5.372 56.884 1462 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.63 % Favored : 95.19 % Rotamer: Outliers : 3.25 % Allowed : 13.64 % Favored : 83.12 % 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: -0.52 (0.46), residues: 124 sheet: -0.29 (0.27), residues: 344 loop : -0.75 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 169 TYR 0.017 0.001 TYR B 204 PHE 0.009 0.001 PHE A 589 TRP 0.012 0.001 TRP A 266 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8768) covalent geometry : angle 0.57024 (11928) SS BOND : bond 0.00711 ( 19) SS BOND : angle 1.75509 ( 38) hydrogen bonds : bond 0.03198 ( 272) hydrogen bonds : angle 6.23853 ( 726) link_BETA1-4 : bond 0.00644 ( 6) link_BETA1-4 : angle 2.35554 ( 18) link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 1.60252 ( 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 74 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 44 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 144 MET cc_start: 0.9150 (ttm) cc_final: 0.8856 (ttt) REVERT: B 213 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8669 (ttm) REVERT: B 406 ILE cc_start: 0.8713 (pt) cc_final: 0.8374 (pp) REVERT: B 455 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.9061 (m) outliers start: 30 outliers final: 14 residues processed: 70 average time/residue: 0.4790 time to fit residues: 36.5797 Evaluate side-chains 56 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 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 593 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 405 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3662 r_free = 0.3662 target = 0.096921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.060418 restraints weight = 17842.366| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.75 r_work: 0.2784 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 8797 Z= 0.215 Angle : 0.623 15.229 11996 Z= 0.310 Chirality : 0.046 0.167 1361 Planarity : 0.004 0.047 1562 Dihedral : 5.168 59.392 1462 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.81 % Favored : 95.01 % Rotamer: Outliers : 3.35 % Allowed : 13.74 % Favored : 82.90 % 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: -0.54 (0.46), residues: 124 sheet: -0.37 (0.26), residues: 351 loop : -0.82 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 543 TYR 0.012 0.001 TYR A 411 PHE 0.011 0.001 PHE B 274 TRP 0.013 0.001 TRP A 266 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 8768) covalent geometry : angle 0.60818 (11928) SS BOND : bond 0.00560 ( 19) SS BOND : angle 1.81435 ( 38) hydrogen bonds : bond 0.03313 ( 272) hydrogen bonds : angle 6.17218 ( 726) link_BETA1-4 : bond 0.00508 ( 6) link_BETA1-4 : angle 2.13354 ( 18) link_NAG-ASN : bond 0.00161 ( 4) link_NAG-ASN : angle 1.62887 ( 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 70 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 39 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.8556 (pmm) cc_final: 0.8331 (pmm) REVERT: B 144 MET cc_start: 0.9271 (ttm) cc_final: 0.8930 (ttt) REVERT: B 213 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8739 (ttm) REVERT: B 406 ILE cc_start: 0.8884 (pt) cc_final: 0.8539 (pp) REVERT: B 455 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9090 (m) outliers start: 31 outliers final: 19 residues processed: 67 average time/residue: 0.4924 time to fit residues: 35.9882 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 : 0.406 ------------------------------------------------------------------------------- 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 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 429 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: 2.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 107 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3665 r_free = 0.3665 target = 0.097105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060698 restraints weight = 17658.907| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.73 r_work: 0.2789 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 8797 Z= 0.194 Angle : 0.615 15.560 11996 Z= 0.306 Chirality : 0.045 0.185 1361 Planarity : 0.004 0.043 1562 Dihedral : 5.020 59.231 1462 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 3.03 % Allowed : 14.50 % Favored : 82.47 % 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: -0.47 (0.46), residues: 124 sheet: -0.35 (0.26), residues: 351 loop : -0.82 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 34 TYR 0.012 0.001 TYR A 411 PHE 0.011 0.001 PHE B 274 TRP 0.013 0.001 TRP A 266 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8768) covalent geometry : angle 0.60280 (11928) SS BOND : bond 0.00603 ( 19) SS BOND : angle 1.71822 ( 38) hydrogen bonds : bond 0.03167 ( 272) hydrogen bonds : angle 6.04441 ( 726) link_BETA1-4 : bond 0.00502 ( 6) link_BETA1-4 : angle 1.82918 ( 18) link_NAG-ASN : bond 0.00124 ( 4) link_NAG-ASN : angle 1.54607 ( 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 66 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8937 (mm) REVERT: B 144 MET cc_start: 0.9276 (ttm) cc_final: 0.8928 (ttt) REVERT: B 213 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8713 (ttm) REVERT: B 455 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9060 (m) outliers start: 28 outliers final: 18 residues processed: 63 average time/residue: 0.5113 time to fit residues: 35.1909 Evaluate side-chains 58 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 499 CYS 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: 2.9990 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 22 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3683 r_free = 0.3683 target = 0.098208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.061951 restraints weight = 17919.356| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.71 r_work: 0.2823 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8797 Z= 0.134 Angle : 0.603 15.621 11996 Z= 0.298 Chirality : 0.045 0.185 1361 Planarity : 0.003 0.048 1562 Dihedral : 4.789 58.184 1461 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 3.03 % Allowed : 15.04 % Favored : 81.93 % 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: -0.84 (0.25), residues: 1102 helix: -0.24 (0.48), residues: 124 sheet: -0.21 (0.27), residues: 349 loop : -0.78 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 430 TYR 0.011 0.001 TYR B 344 PHE 0.010 0.001 PHE B 274 TRP 0.013 0.001 TRP A 266 HIS 0.003 0.000 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8768) covalent geometry : angle 0.59402 (11928) SS BOND : bond 0.00535 ( 19) SS BOND : angle 1.49774 ( 38) hydrogen bonds : bond 0.02897 ( 272) hydrogen bonds : angle 5.86752 ( 726) link_BETA1-4 : bond 0.00516 ( 6) link_BETA1-4 : angle 1.59138 ( 18) link_NAG-ASN : bond 0.00096 ( 4) link_NAG-ASN : angle 1.48008 ( 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 69 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 41 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8846 (mm) REVERT: B 30 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8936 (tt) REVERT: B 144 MET cc_start: 0.9242 (ttm) cc_final: 0.8953 (ttt) REVERT: B 213 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8686 (ttm) REVERT: B 455 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9094 (m) outliers start: 28 outliers final: 17 residues processed: 63 average time/residue: 0.4870 time to fit residues: 33.5040 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 : 0.346 ------------------------------------------------------------------------------- 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 490 GLN Chi-restraints excluded: chain A residue 504 CYS 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: 0.9990 chunk 1 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3674 r_free = 0.3674 target = 0.097576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061119 restraints weight = 17837.675| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.75 r_work: 0.2797 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1806 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= 0.174 Angle : 0.623 15.298 11996 Z= 0.309 Chirality : 0.046 0.226 1361 Planarity : 0.004 0.045 1562 Dihedral : 4.771 57.224 1461 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 2.71 % Allowed : 15.48 % Favored : 81.82 % 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: -0.24 (0.47), residues: 124 sheet: -0.28 (0.26), residues: 353 loop : -0.76 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 169 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 covalent geometry : bond 0.00415 ( 8768) covalent geometry : angle 0.61401 (11928) SS BOND : bond 0.00541 ( 19) SS BOND : angle 1.55759 ( 38) hydrogen bonds : bond 0.03086 ( 272) hydrogen bonds : angle 5.91902 ( 726) link_BETA1-4 : bond 0.00485 ( 6) link_BETA1-4 : angle 1.59012 ( 18) link_NAG-ASN : bond 0.00118 ( 4) link_NAG-ASN : angle 1.49474 ( 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: 25 poor density : 40 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8963 (mm) REVERT: B 144 MET cc_start: 0.9256 (ttm) cc_final: 0.8963 (ttt) REVERT: B 213 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8712 (ttm) REVERT: B 455 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.9072 (m) outliers start: 25 outliers final: 18 residues processed: 60 average time/residue: 0.4846 time to fit residues: 31.7241 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 : 0.332 ------------------------------------------------------------------------------- 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 490 GLN 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 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 233 VAL 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: 0.6980 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.097814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.061481 restraints weight = 17716.228| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.71 r_work: 0.2819 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8797 Z= 0.156 Angle : 0.623 14.666 11996 Z= 0.309 Chirality : 0.045 0.195 1361 Planarity : 0.004 0.048 1562 Dihedral : 4.684 57.023 1460 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 2.71 % Allowed : 15.48 % Favored : 81.82 % 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: -0.16 (0.48), residues: 124 sheet: -0.26 (0.27), residues: 354 loop : -0.80 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 169 TYR 0.011 0.001 TYR B 344 PHE 0.011 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 covalent geometry : bond 0.00375 ( 8768) covalent geometry : angle 0.61520 (11928) SS BOND : bond 0.00519 ( 19) SS BOND : angle 1.49112 ( 38) hydrogen bonds : bond 0.03053 ( 272) hydrogen bonds : angle 5.85397 ( 726) link_BETA1-4 : bond 0.00494 ( 6) link_BETA1-4 : angle 1.45815 ( 18) link_NAG-ASN : bond 0.00095 ( 4) link_NAG-ASN : angle 1.43667 ( 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: 25 poor density : 39 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8922 (mm) REVERT: B 34 ARG cc_start: 0.9167 (tpp80) cc_final: 0.8552 (ttp-170) REVERT: B 144 MET cc_start: 0.9268 (ttm) cc_final: 0.8978 (ttt) REVERT: B 213 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8683 (ttm) REVERT: B 455 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9095 (m) outliers start: 25 outliers final: 18 residues processed: 60 average time/residue: 0.4801 time to fit residues: 31.3966 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 : 0.343 ------------------------------------------------------------------------------- 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 490 GLN 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 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 233 VAL 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 69 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 109 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3680 r_free = 0.3680 target = 0.097806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.061524 restraints weight = 17656.068| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.69 r_work: 0.2823 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8797 Z= 0.147 Angle : 0.629 15.805 11996 Z= 0.313 Chirality : 0.045 0.212 1361 Planarity : 0.004 0.047 1562 Dihedral : 4.626 57.019 1460 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 2.16 % Allowed : 16.13 % Favored : 81.71 % 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: -0.84 (0.25), residues: 1102 helix: -0.16 (0.48), residues: 125 sheet: -0.19 (0.27), residues: 353 loop : -0.81 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 430 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 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8768) covalent geometry : angle 0.62148 (11928) SS BOND : bond 0.00459 ( 19) SS BOND : angle 1.46092 ( 38) hydrogen bonds : bond 0.03031 ( 272) hydrogen bonds : angle 5.78202 ( 726) link_BETA1-4 : bond 0.00484 ( 6) link_BETA1-4 : angle 1.41611 ( 18) link_NAG-ASN : bond 0.00090 ( 4) link_NAG-ASN : angle 1.43582 ( 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 60 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8850 (mm) REVERT: B 34 ARG cc_start: 0.9170 (tpp80) cc_final: 0.8533 (ttp-170) REVERT: B 144 MET cc_start: 0.9269 (ttm) cc_final: 0.8984 (ttt) REVERT: B 213 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8678 (ttm) REVERT: B 455 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9080 (m) outliers start: 20 outliers final: 16 residues processed: 56 average time/residue: 0.5684 time to fit residues: 34.4506 Evaluate side-chains 57 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 490 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 0.0060 chunk 95 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3687 r_free = 0.3687 target = 0.098178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062030 restraints weight = 17647.741| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.70 r_work: 0.2832 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8797 Z= 0.135 Angle : 0.632 15.444 11996 Z= 0.312 Chirality : 0.045 0.197 1361 Planarity : 0.004 0.048 1562 Dihedral : 4.596 56.903 1460 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 2.27 % Allowed : 16.13 % Favored : 81.60 % 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: -0.82 (0.25), residues: 1102 helix: -0.15 (0.48), residues: 126 sheet: -0.16 (0.27), residues: 353 loop : -0.81 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 430 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 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8768) covalent geometry : angle 0.62520 (11928) SS BOND : bond 0.00528 ( 19) SS BOND : angle 1.41328 ( 38) hydrogen bonds : bond 0.02948 ( 272) hydrogen bonds : angle 5.73894 ( 726) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 1.37184 ( 18) link_NAG-ASN : bond 0.00086 ( 4) link_NAG-ASN : angle 1.41081 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3667.60 seconds wall clock time: 63 minutes 21.85 seconds (3801.85 seconds total)