Starting phenix.real_space_refine on Wed Mar 4 00:02:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ujb_20795/03_2026/6ujb_20795.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ujb_20795/03_2026/6ujb_20795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ujb_20795/03_2026/6ujb_20795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ujb_20795/03_2026/6ujb_20795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ujb_20795/03_2026/6ujb_20795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ujb_20795/03_2026/6ujb_20795.map" } resolution = 3.51 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= 0.003 sd= 0.060 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 5 9.91 5 Mg 1 5.21 5 S 43 5.16 5 C 5792 2.51 5 N 1549 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9193 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4387 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 564} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'ARG:plan': 5, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2812 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 898 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.94, per 1000 atoms: 0.21 Number of scatterers: 9193 At special positions: 0 Unit cell: (72.63, 100.875, 165.435, 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 5 19.99 S 43 16.00 Mg 1 11.99 O 1803 8.00 N 1549 7.00 C 5792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.02 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.06 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.05 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " 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 ALPHA1-2 " MAN C 4 " - " MAN C 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A2005 " - " ASN A 260 " " NAG B2005 " - " ASN B 360 " " NAG B2010 " - " ASN B 379 " " NAG C 1 " - " ASN A 266 " " NAG D 1 " - " ASN A 44 " " NAG G 1 " - " ASN B 191 " " NAG H 1 " - " ASN B 389 " " NAG I 1 " - " ASN B 414 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 256.8 milliseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 22 sheets defined 13.6% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.519A pdb=" N VAL B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASN B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.791A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.712A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 4.326A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 100 through 104 removed outlier: 4.313A pdb=" N ASP E 104 " --> pdb=" O TYR E 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.793A pdb=" N LEU F 89 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.200A pdb=" N ARG A 436 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP A 6 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR A 412 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 423 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLY A 410 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY A 425 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET A 408 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.071A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 101 removed outlier: 4.010A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.710A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.516A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.441A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.328A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER A 471 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.328A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.661A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB7, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.298A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.414A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.508A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 345 hydrogen bonds defined for protein. 867 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: 1.51 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1827 1.32 - 1.45: 2418 1.45 - 1.58: 5059 1.58 - 1.71: 9 1.71 - 1.83: 66 Bond restraints: 9379 Sorted by residual: bond pdb=" CB HIS B 184 " pdb=" CG HIS B 184 " ideal model delta sigma weight residual 1.497 1.445 0.052 1.40e-02 5.10e+03 1.37e+01 bond pdb=" CB ASN B 332 " pdb=" CG ASN B 332 " ideal model delta sigma weight residual 1.516 1.430 0.086 2.50e-02 1.60e+03 1.17e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.455 -0.071 2.10e-02 2.27e+03 1.15e+01 bond pdb=" C5 NAG A2005 " pdb=" O5 NAG A2005 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 9374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.77: 12719 7.77 - 15.54: 5 15.54 - 23.30: 0 23.30 - 31.07: 0 31.07 - 38.84: 1 Bond angle restraints: 12725 Sorted by residual: angle pdb=" C2 NAG H 2 " pdb=" N2 NAG H 2 " pdb=" C7 NAG H 2 " ideal model delta sigma weight residual 124.56 163.40 -38.84 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 128.17 -8.61 1.02e+00 9.61e-01 7.12e+01 angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 127.81 -8.25 1.02e+00 9.61e-01 6.54e+01 angle pdb=" C ALA A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta sigma weight residual 119.56 127.41 -7.85 1.02e+00 9.61e-01 5.93e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.40 -7.84 1.02e+00 9.61e-01 5.91e+01 ... (remaining 12720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.42: 5640 21.42 - 42.83: 122 42.83 - 64.25: 37 64.25 - 85.67: 17 85.67 - 107.08: 7 Dihedral angle restraints: 5823 sinusoidal: 2433 harmonic: 3390 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 40.72 52.28 1 1.00e+01 1.00e-02 3.73e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 94 " pdb=" CB CYS F 94 " ideal model delta sinusoidal sigma weight residual 93.00 52.10 40.90 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CA TYR B 103 " pdb=" C TYR B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 5820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1000 0.071 - 0.141: 343 0.141 - 0.212: 61 0.212 - 0.283: 32 0.283 - 0.354: 18 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.44e+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 -2.29 -0.11 2.00e-02 2.50e+03 3.07e+01 chirality pdb=" C1 MAN C 5 " pdb=" O2 MAN C 4 " pdb=" C2 MAN C 5 " pdb=" O5 MAN C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 7.47e+00 ... (remaining 1451 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 260 " 0.030 2.00e-02 2.50e+03 3.12e-02 1.22e+01 pdb=" CG ASN A 260 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 260 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 260 " -0.048 2.00e-02 2.50e+03 pdb=" C1 NAG A2005 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 379 " -0.023 2.00e-02 2.50e+03 2.44e-02 7.46e+00 pdb=" CG ASN B 379 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 379 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 379 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG B2010 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 44 " -0.021 2.00e-02 2.50e+03 2.26e-02 6.40e+00 pdb=" CG ASN A 44 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 44 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 44 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.028 2.00e-02 2.50e+03 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 25 2.41 - 3.03: 5542 3.03 - 3.65: 12893 3.65 - 4.28: 21698 4.28 - 4.90: 34934 Nonbonded interactions: 75092 Sorted by model distance: nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.782 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 1.955 2.170 nonbonded pdb=" OD2 ASP B 151 " pdb="CA CA B2001 " model vdw 2.095 2.510 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A2003 " model vdw 2.099 2.510 nonbonded pdb=" OD1 ASP B 209 " pdb="CA CA B2001 " model vdw 2.104 2.510 ... (remaining 75087 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 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 group one per residue 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.090 Find NCS groups from input model: 0.050 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.015 0.086 9405 Z= 0.790 Angle : 1.455 38.841 12794 Z= 0.955 Chirality : 0.084 0.354 1454 Planarity : 0.006 0.027 1645 Dihedral : 11.747 107.084 3628 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 0.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.55 (0.23), residues: 1170 helix: -1.33 (0.43), residues: 97 sheet: 1.03 (0.23), residues: 429 loop : 0.29 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 231 TYR 0.034 0.005 TYR A 254 PHE 0.021 0.004 PHE A 276 TRP 0.023 0.006 TRP A 179 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.01440 ( 9379) covalent geometry : angle 1.44549 (12725) SS BOND : bond 0.01432 ( 9) SS BOND : angle 1.85822 ( 18) hydrogen bonds : bond 0.16218 ( 331) hydrogen bonds : angle 8.74887 ( 867) link_ALPHA1-2 : bond 0.07545 ( 1) link_ALPHA1-2 : angle 3.73079 ( 3) link_ALPHA1-3 : bond 0.07384 ( 1) link_ALPHA1-3 : angle 3.21876 ( 3) link_ALPHA1-6 : bond 0.05592 ( 1) link_ALPHA1-6 : angle 3.04015 ( 3) link_BETA1-4 : bond 0.06287 ( 6) link_BETA1-4 : angle 3.32913 ( 18) link_NAG-ASN : bond 0.06410 ( 8) link_NAG-ASN : angle 2.20889 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7791 (t0) cc_final: 0.7577 (t0) REVERT: A 191 ILE cc_start: 0.8818 (mt) cc_final: 0.7931 (mt) REVERT: A 408 MET cc_start: 0.8061 (mtm) cc_final: 0.7859 (mtm) REVERT: B 117 MET cc_start: 0.9137 (mmm) cc_final: 0.8853 (mmm) REVERT: B 135 MET cc_start: 0.8005 (mmm) cc_final: 0.7788 (mmm) REVERT: E 43 LYS cc_start: 0.8263 (mttt) cc_final: 0.7989 (mppt) REVERT: E 50 ARG cc_start: 0.7998 (ptm-80) cc_final: 0.7746 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1281 time to fit residues: 29.8574 Evaluate side-chains 91 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 377 ASN B 166 HIS ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103377 restraints weight = 15255.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106174 restraints weight = 9036.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107968 restraints weight = 6457.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109141 restraints weight = 5159.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109808 restraints weight = 4422.517| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9405 Z= 0.180 Angle : 0.654 8.942 12794 Z= 0.340 Chirality : 0.048 0.263 1454 Planarity : 0.004 0.038 1645 Dihedral : 7.839 88.800 1617 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.61 % Allowed : 6.77 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.44 (0.24), residues: 1170 helix: -0.38 (0.50), residues: 96 sheet: 0.64 (0.23), residues: 464 loop : 0.27 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 133 TYR 0.015 0.002 TYR A 561 PHE 0.014 0.002 PHE F 68 TRP 0.012 0.002 TRP A 61 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9379) covalent geometry : angle 0.63501 (12725) SS BOND : bond 0.00280 ( 9) SS BOND : angle 1.65307 ( 18) hydrogen bonds : bond 0.04064 ( 331) hydrogen bonds : angle 6.77450 ( 867) link_ALPHA1-2 : bond 0.00642 ( 1) link_ALPHA1-2 : angle 1.54218 ( 3) link_ALPHA1-3 : bond 0.01509 ( 1) link_ALPHA1-3 : angle 1.40027 ( 3) link_ALPHA1-6 : bond 0.01166 ( 1) link_ALPHA1-6 : angle 1.31316 ( 3) link_BETA1-4 : bond 0.01266 ( 6) link_BETA1-4 : angle 3.08570 ( 18) link_NAG-ASN : bond 0.00496 ( 8) link_NAG-ASN : angle 1.99408 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.9263 (t) cc_final: 0.9030 (p) REVERT: A 408 MET cc_start: 0.8040 (mtm) cc_final: 0.7740 (mtm) REVERT: B 135 MET cc_start: 0.8330 (mmm) cc_final: 0.8003 (mmm) REVERT: E 13 LYS cc_start: 0.6600 (mmtt) cc_final: 0.6303 (mmtt) REVERT: E 43 LYS cc_start: 0.8268 (mttt) cc_final: 0.8051 (mppt) outliers start: 15 outliers final: 10 residues processed: 102 average time/residue: 0.0912 time to fit residues: 13.0437 Evaluate side-chains 87 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 0.0010 chunk 72 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 63 HIS B 383 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100832 restraints weight = 15073.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103730 restraints weight = 8652.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105580 restraints weight = 6070.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.106662 restraints weight = 4792.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107489 restraints weight = 4123.437| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9405 Z= 0.132 Angle : 0.566 8.111 12794 Z= 0.293 Chirality : 0.046 0.284 1454 Planarity : 0.004 0.039 1645 Dihedral : 6.821 77.116 1617 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.29 % Allowed : 8.59 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.49 (0.24), residues: 1170 helix: -0.00 (0.52), residues: 96 sheet: 0.83 (0.24), residues: 435 loop : 0.11 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 211 TYR 0.024 0.001 TYR E 100 PHE 0.011 0.001 PHE F 68 TRP 0.024 0.002 TRP A 61 HIS 0.010 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9379) covalent geometry : angle 0.55143 (12725) SS BOND : bond 0.00263 ( 9) SS BOND : angle 0.88901 ( 18) hydrogen bonds : bond 0.03314 ( 331) hydrogen bonds : angle 6.14766 ( 867) link_ALPHA1-2 : bond 0.00646 ( 1) link_ALPHA1-2 : angle 1.33213 ( 3) link_ALPHA1-3 : bond 0.01065 ( 1) link_ALPHA1-3 : angle 1.77012 ( 3) link_ALPHA1-6 : bond 0.01189 ( 1) link_ALPHA1-6 : angle 1.23203 ( 3) link_BETA1-4 : bond 0.01158 ( 6) link_BETA1-4 : angle 2.61374 ( 18) link_NAG-ASN : bond 0.00578 ( 8) link_NAG-ASN : angle 1.74750 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.9236 (t) cc_final: 0.8996 (p) REVERT: A 261 MET cc_start: 0.9012 (mmt) cc_final: 0.8811 (tpp) REVERT: A 408 MET cc_start: 0.8091 (mtm) cc_final: 0.7801 (mtm) REVERT: B 117 MET cc_start: 0.9271 (mmm) cc_final: 0.8916 (mmm) REVERT: B 278 MET cc_start: 0.8583 (mtm) cc_final: 0.8265 (mtm) REVERT: B 394 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7007 (ttp) REVERT: E 31 ASP cc_start: 0.6819 (m-30) cc_final: 0.6576 (m-30) REVERT: E 80 TYR cc_start: 0.8197 (m-80) cc_final: 0.7978 (m-80) REVERT: E 100 TYR cc_start: 0.8778 (t80) cc_final: 0.8530 (t80) REVERT: F 34 THR cc_start: 0.9131 (p) cc_final: 0.8818 (m) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.1061 time to fit residues: 14.0857 Evaluate side-chains 88 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN E 35 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096070 restraints weight = 15183.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098843 restraints weight = 8904.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100627 restraints weight = 6343.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101807 restraints weight = 5070.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102458 restraints weight = 4342.059| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9405 Z= 0.225 Angle : 0.603 8.570 12794 Z= 0.307 Chirality : 0.048 0.315 1454 Planarity : 0.004 0.038 1645 Dihedral : 6.573 70.093 1617 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.50 % Allowed : 8.70 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.21 (0.24), residues: 1170 helix: -0.18 (0.53), residues: 96 sheet: 0.60 (0.23), residues: 445 loop : -0.06 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 35 TYR 0.016 0.001 TYR F 55 PHE 0.021 0.002 PHE A 427 TRP 0.016 0.002 TRP A 61 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 9379) covalent geometry : angle 0.58724 (12725) SS BOND : bond 0.00377 ( 9) SS BOND : angle 1.04404 ( 18) hydrogen bonds : bond 0.03392 ( 331) hydrogen bonds : angle 5.96357 ( 867) link_ALPHA1-2 : bond 0.00533 ( 1) link_ALPHA1-2 : angle 1.29948 ( 3) link_ALPHA1-3 : bond 0.01084 ( 1) link_ALPHA1-3 : angle 1.91410 ( 3) link_ALPHA1-6 : bond 0.01176 ( 1) link_ALPHA1-6 : angle 1.23090 ( 3) link_BETA1-4 : bond 0.01120 ( 6) link_BETA1-4 : angle 2.83797 ( 18) link_NAG-ASN : bond 0.00365 ( 8) link_NAG-ASN : angle 1.81348 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8163 (mtm) cc_final: 0.7913 (mtm) REVERT: B 278 MET cc_start: 0.8655 (mtm) cc_final: 0.8418 (mtm) REVERT: B 394 MET cc_start: 0.7514 (ttm) cc_final: 0.7187 (ttp) REVERT: E 80 TYR cc_start: 0.8072 (m-80) cc_final: 0.7825 (m-10) REVERT: E 100 TYR cc_start: 0.8874 (t80) cc_final: 0.8663 (t80) REVERT: F 35 ARG cc_start: 0.8327 (mtt90) cc_final: 0.8034 (mtm-85) outliers start: 14 outliers final: 10 residues processed: 90 average time/residue: 0.1076 time to fit residues: 13.4590 Evaluate side-chains 85 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 82 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** 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 = 0.3600 r_free = 0.3600 target = 0.118240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097522 restraints weight = 15005.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100318 restraints weight = 8736.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102114 restraints weight = 6200.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103135 restraints weight = 4928.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103989 restraints weight = 4268.586| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9405 Z= 0.133 Angle : 0.533 7.812 12794 Z= 0.273 Chirality : 0.046 0.309 1454 Planarity : 0.004 0.037 1645 Dihedral : 6.205 65.200 1617 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.18 % Allowed : 9.13 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.22 (0.24), residues: 1170 helix: -0.07 (0.54), residues: 96 sheet: 0.62 (0.24), residues: 436 loop : -0.07 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 35 TYR 0.012 0.001 TYR A 254 PHE 0.011 0.001 PHE A 427 TRP 0.016 0.001 TRP A 61 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9379) covalent geometry : angle 0.52034 (12725) SS BOND : bond 0.00235 ( 9) SS BOND : angle 0.73975 ( 18) hydrogen bonds : bond 0.02885 ( 331) hydrogen bonds : angle 5.74649 ( 867) link_ALPHA1-2 : bond 0.00582 ( 1) link_ALPHA1-2 : angle 1.31633 ( 3) link_ALPHA1-3 : bond 0.01119 ( 1) link_ALPHA1-3 : angle 2.00469 ( 3) link_ALPHA1-6 : bond 0.01133 ( 1) link_ALPHA1-6 : angle 1.24107 ( 3) link_BETA1-4 : bond 0.01032 ( 6) link_BETA1-4 : angle 2.43161 ( 18) link_NAG-ASN : bond 0.00364 ( 8) link_NAG-ASN : angle 1.50704 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: B 278 MET cc_start: 0.8547 (mtm) cc_final: 0.8313 (mtm) REVERT: B 394 MET cc_start: 0.7395 (ttm) cc_final: 0.7070 (ttp) REVERT: E 13 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6511 (mmtt) REVERT: E 80 TYR cc_start: 0.8056 (m-80) cc_final: 0.7831 (m-10) REVERT: E 100 TYR cc_start: 0.8731 (t80) cc_final: 0.8509 (t80) REVERT: F 4 MET cc_start: 0.8678 (mmm) cc_final: 0.8394 (mmm) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 0.1035 time to fit residues: 12.8876 Evaluate side-chains 82 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096164 restraints weight = 15256.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098938 restraints weight = 9056.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.100749 restraints weight = 6498.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.101892 restraints weight = 5209.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102575 restraints weight = 4484.068| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9405 Z= 0.160 Angle : 0.550 7.939 12794 Z= 0.280 Chirality : 0.046 0.309 1454 Planarity : 0.004 0.038 1645 Dihedral : 6.049 61.399 1617 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.50 % Allowed : 9.34 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.10 (0.24), residues: 1170 helix: -0.18 (0.53), residues: 97 sheet: 0.52 (0.24), residues: 438 loop : -0.13 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 35 TYR 0.013 0.001 TYR A 254 PHE 0.014 0.001 PHE A 427 TRP 0.012 0.001 TRP A 61 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9379) covalent geometry : angle 0.53645 (12725) SS BOND : bond 0.00242 ( 9) SS BOND : angle 0.85254 ( 18) hydrogen bonds : bond 0.02983 ( 331) hydrogen bonds : angle 5.65236 ( 867) link_ALPHA1-2 : bond 0.00587 ( 1) link_ALPHA1-2 : angle 1.30841 ( 3) link_ALPHA1-3 : bond 0.01127 ( 1) link_ALPHA1-3 : angle 2.08028 ( 3) link_ALPHA1-6 : bond 0.01093 ( 1) link_ALPHA1-6 : angle 1.21474 ( 3) link_BETA1-4 : bond 0.00998 ( 6) link_BETA1-4 : angle 2.48669 ( 18) link_NAG-ASN : bond 0.00280 ( 8) link_NAG-ASN : angle 1.54860 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: B 278 MET cc_start: 0.8553 (mtm) cc_final: 0.8325 (mtm) REVERT: B 394 MET cc_start: 0.7456 (ttm) cc_final: 0.7132 (ttp) REVERT: E 80 TYR cc_start: 0.8190 (m-80) cc_final: 0.7977 (m-10) REVERT: F 42 TYR cc_start: 0.9339 (m-80) cc_final: 0.8833 (m-10) outliers start: 14 outliers final: 12 residues processed: 85 average time/residue: 0.0970 time to fit residues: 11.9732 Evaluate side-chains 87 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 59 optimal weight: 0.0270 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096628 restraints weight = 15179.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099426 restraints weight = 8902.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101174 restraints weight = 6330.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102292 restraints weight = 5083.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103045 restraints weight = 4367.289| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9405 Z= 0.144 Angle : 0.540 7.850 12794 Z= 0.274 Chirality : 0.046 0.301 1454 Planarity : 0.004 0.037 1645 Dihedral : 5.849 57.326 1617 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.50 % Allowed : 9.56 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.09 (0.24), residues: 1170 helix: -0.16 (0.53), residues: 97 sheet: 0.50 (0.23), residues: 443 loop : -0.13 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.012 0.001 TYR A 254 PHE 0.012 0.001 PHE A 427 TRP 0.012 0.001 TRP A 61 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9379) covalent geometry : angle 0.52762 (12725) SS BOND : bond 0.00235 ( 9) SS BOND : angle 0.84953 ( 18) hydrogen bonds : bond 0.02816 ( 331) hydrogen bonds : angle 5.57425 ( 867) link_ALPHA1-2 : bond 0.00594 ( 1) link_ALPHA1-2 : angle 1.29812 ( 3) link_ALPHA1-3 : bond 0.01136 ( 1) link_ALPHA1-3 : angle 2.07646 ( 3) link_ALPHA1-6 : bond 0.01111 ( 1) link_ALPHA1-6 : angle 1.20436 ( 3) link_BETA1-4 : bond 0.01006 ( 6) link_BETA1-4 : angle 2.38480 ( 18) link_NAG-ASN : bond 0.00253 ( 8) link_NAG-ASN : angle 1.49292 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 278 MET cc_start: 0.8537 (mtm) cc_final: 0.8312 (mtm) REVERT: B 394 MET cc_start: 0.7436 (ttm) cc_final: 0.7125 (ttp) REVERT: E 11 LEU cc_start: 0.7221 (tt) cc_final: 0.6814 (mp) REVERT: E 80 TYR cc_start: 0.8211 (m-80) cc_final: 0.7975 (m-10) REVERT: E 104 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7930 (p0) REVERT: F 42 TYR cc_start: 0.9331 (m-80) cc_final: 0.8780 (m-10) outliers start: 14 outliers final: 11 residues processed: 88 average time/residue: 0.0966 time to fit residues: 12.2468 Evaluate side-chains 84 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 75 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095822 restraints weight = 15025.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098562 restraints weight = 8887.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100298 restraints weight = 6368.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101434 restraints weight = 5122.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102066 restraints weight = 4402.597| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9405 Z= 0.161 Angle : 0.550 7.877 12794 Z= 0.279 Chirality : 0.046 0.298 1454 Planarity : 0.004 0.038 1645 Dihedral : 5.719 53.892 1617 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.61 % Allowed : 9.88 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.03 (0.24), residues: 1170 helix: -0.19 (0.53), residues: 97 sheet: 0.43 (0.23), residues: 443 loop : -0.15 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 35 TYR 0.013 0.001 TYR A 254 PHE 0.016 0.001 PHE A 427 TRP 0.023 0.002 TRP A 61 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9379) covalent geometry : angle 0.53712 (12725) SS BOND : bond 0.00285 ( 9) SS BOND : angle 1.09541 ( 18) hydrogen bonds : bond 0.02877 ( 331) hydrogen bonds : angle 5.54392 ( 867) link_ALPHA1-2 : bond 0.00613 ( 1) link_ALPHA1-2 : angle 1.29233 ( 3) link_ALPHA1-3 : bond 0.01090 ( 1) link_ALPHA1-3 : angle 2.08310 ( 3) link_ALPHA1-6 : bond 0.01082 ( 1) link_ALPHA1-6 : angle 1.18200 ( 3) link_BETA1-4 : bond 0.00966 ( 6) link_BETA1-4 : angle 2.39989 ( 18) link_NAG-ASN : bond 0.00290 ( 8) link_NAG-ASN : angle 1.52328 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: B 278 MET cc_start: 0.8530 (mtm) cc_final: 0.8289 (mtm) REVERT: B 394 MET cc_start: 0.7478 (ttm) cc_final: 0.7173 (ttp) REVERT: E 11 LEU cc_start: 0.7318 (tt) cc_final: 0.6947 (mp) REVERT: E 80 TYR cc_start: 0.8229 (m-80) cc_final: 0.8007 (m-10) REVERT: E 104 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8070 (p0) REVERT: F 4 MET cc_start: 0.8642 (mmm) cc_final: 0.8157 (tpt) REVERT: F 42 TYR cc_start: 0.9332 (m-80) cc_final: 0.8847 (m-10) outliers start: 15 outliers final: 13 residues processed: 88 average time/residue: 0.1042 time to fit residues: 13.0045 Evaluate side-chains 88 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095381 restraints weight = 15349.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098131 restraints weight = 9077.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099920 restraints weight = 6511.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100946 restraints weight = 5229.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101782 restraints weight = 4544.463| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9405 Z= 0.153 Angle : 0.547 7.834 12794 Z= 0.278 Chirality : 0.046 0.287 1454 Planarity : 0.004 0.039 1645 Dihedral : 5.571 50.568 1617 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.72 % Allowed : 9.99 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.01 (0.24), residues: 1170 helix: -0.17 (0.53), residues: 97 sheet: 0.41 (0.23), residues: 440 loop : -0.17 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.013 0.001 TYR A 254 PHE 0.015 0.001 PHE A 427 TRP 0.029 0.002 TRP A 61 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9379) covalent geometry : angle 0.53476 (12725) SS BOND : bond 0.00252 ( 9) SS BOND : angle 0.95780 ( 18) hydrogen bonds : bond 0.02791 ( 331) hydrogen bonds : angle 5.51762 ( 867) link_ALPHA1-2 : bond 0.00650 ( 1) link_ALPHA1-2 : angle 1.30805 ( 3) link_ALPHA1-3 : bond 0.01155 ( 1) link_ALPHA1-3 : angle 2.14200 ( 3) link_ALPHA1-6 : bond 0.01081 ( 1) link_ALPHA1-6 : angle 1.17478 ( 3) link_BETA1-4 : bond 0.00984 ( 6) link_BETA1-4 : angle 2.34071 ( 18) link_NAG-ASN : bond 0.00226 ( 8) link_NAG-ASN : angle 1.49587 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 172 TYR cc_start: 0.8110 (m-80) cc_final: 0.7864 (m-80) REVERT: B 278 MET cc_start: 0.8517 (mtm) cc_final: 0.8273 (mtm) REVERT: B 394 MET cc_start: 0.7474 (ttm) cc_final: 0.7195 (ttp) REVERT: E 11 LEU cc_start: 0.7432 (tt) cc_final: 0.7133 (mp) REVERT: E 80 TYR cc_start: 0.8233 (m-80) cc_final: 0.8004 (m-10) REVERT: E 104 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8078 (p0) REVERT: F 4 MET cc_start: 0.8753 (mmm) cc_final: 0.8123 (tpt) REVERT: F 42 TYR cc_start: 0.9333 (m-80) cc_final: 0.8846 (m-10) outliers start: 16 outliers final: 14 residues processed: 91 average time/residue: 0.0969 time to fit residues: 12.6514 Evaluate side-chains 90 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.083947 restraints weight = 16001.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.085903 restraints weight = 10888.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.087180 restraints weight = 8451.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.087969 restraints weight = 7104.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.088621 restraints weight = 6365.158| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9405 Z= 0.169 Angle : 0.565 7.720 12794 Z= 0.287 Chirality : 0.047 0.282 1454 Planarity : 0.004 0.040 1645 Dihedral : 5.485 47.414 1617 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.61 % Allowed : 10.10 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -0.04 (0.24), residues: 1170 helix: -0.25 (0.53), residues: 97 sheet: 0.37 (0.24), residues: 440 loop : -0.18 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 35 TYR 0.014 0.001 TYR A 254 PHE 0.017 0.001 PHE A 427 TRP 0.038 0.002 TRP A 61 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9379) covalent geometry : angle 0.55224 (12725) SS BOND : bond 0.00255 ( 9) SS BOND : angle 1.01057 ( 18) hydrogen bonds : bond 0.02864 ( 331) hydrogen bonds : angle 5.53714 ( 867) link_ALPHA1-2 : bond 0.00667 ( 1) link_ALPHA1-2 : angle 1.31030 ( 3) link_ALPHA1-3 : bond 0.01148 ( 1) link_ALPHA1-3 : angle 2.15471 ( 3) link_ALPHA1-6 : bond 0.01061 ( 1) link_ALPHA1-6 : angle 1.16382 ( 3) link_BETA1-4 : bond 0.00908 ( 6) link_BETA1-4 : angle 2.32795 ( 18) link_NAG-ASN : bond 0.00259 ( 8) link_NAG-ASN : angle 1.56035 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 278 MET cc_start: 0.8579 (mtm) cc_final: 0.8364 (mtm) REVERT: B 394 MET cc_start: 0.7463 (ttm) cc_final: 0.7214 (ttp) REVERT: E 11 LEU cc_start: 0.7290 (tt) cc_final: 0.7012 (mp) REVERT: E 80 TYR cc_start: 0.8232 (m-80) cc_final: 0.7993 (m-10) REVERT: E 104 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7987 (p0) REVERT: F 42 TYR cc_start: 0.9311 (m-80) cc_final: 0.8839 (m-10) outliers start: 15 outliers final: 13 residues processed: 85 average time/residue: 0.0917 time to fit residues: 11.3752 Evaluate side-chains 88 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** 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 = 0.3317 r_free = 0.3317 target = 0.103175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.083570 restraints weight = 15933.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.085497 restraints weight = 10918.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.086771 restraints weight = 8493.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.087509 restraints weight = 7174.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.088139 restraints weight = 6428.195| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9405 Z= 0.181 Angle : 0.573 7.797 12794 Z= 0.292 Chirality : 0.047 0.273 1454 Planarity : 0.004 0.041 1645 Dihedral : 5.451 45.290 1617 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.83 % Allowed : 9.99 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -0.16 (0.24), residues: 1170 helix: -0.34 (0.53), residues: 97 sheet: 0.27 (0.23), residues: 443 loop : -0.24 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 35 TYR 0.015 0.001 TYR A 254 PHE 0.018 0.001 PHE A 427 TRP 0.040 0.002 TRP A 61 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9379) covalent geometry : angle 0.56085 (12725) SS BOND : bond 0.00232 ( 9) SS BOND : angle 0.91502 ( 18) hydrogen bonds : bond 0.02922 ( 331) hydrogen bonds : angle 5.53387 ( 867) link_ALPHA1-2 : bond 0.00679 ( 1) link_ALPHA1-2 : angle 1.30912 ( 3) link_ALPHA1-3 : bond 0.01102 ( 1) link_ALPHA1-3 : angle 2.17472 ( 3) link_ALPHA1-6 : bond 0.01042 ( 1) link_ALPHA1-6 : angle 1.16119 ( 3) link_BETA1-4 : bond 0.00952 ( 6) link_BETA1-4 : angle 2.29250 ( 18) link_NAG-ASN : bond 0.00428 ( 8) link_NAG-ASN : angle 1.73410 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1525.84 seconds wall clock time: 27 minutes 10.94 seconds (1630.94 seconds total)