Starting phenix.real_space_refine on Tue Mar 3 18:55:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f55_31458/03_2026/7f55_31458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f55_31458/03_2026/7f55_31458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f55_31458/03_2026/7f55_31458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f55_31458/03_2026/7f55_31458.map" model { file = "/net/cci-nas-00/data/ceres_data/7f55_31458/03_2026/7f55_31458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f55_31458/03_2026/7f55_31458.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 62 5.16 5 C 5127 2.51 5 N 1397 2.21 5 O 1501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 8088 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1885 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2133 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 2 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 1.70, per 1000 atoms: 0.21 Number of scatterers: 8088 At special positions: 0 Unit cell: (86.19, 95.316, 122.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 62 16.00 O 1501 8.00 N 1397 7.00 C 5127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.04 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.02 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=1, symmetry=0 Links applied TRANS " DPN L 4 " - " HIS L 3 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 319.1 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN L 4 " Number of C-beta restraints generated: 1938 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.837A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.527A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.457A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.556A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 47 through 71 removed outlier: 3.827A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 110 Processing helix chain 'R' and resid 117 through 153 removed outlier: 3.547A pdb=" N SER R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 160 Processing helix chain 'R' and resid 162 through 187 Processing helix chain 'R' and resid 190 through 228 removed outlier: 3.916A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.734A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.621A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 removed outlier: 3.920A pdb=" N ILE R 289 " --> pdb=" O ASN R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 302 removed outlier: 3.629A pdb=" N TYR R 302 " --> pdb=" O PRO R 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 299 through 302' Processing helix chain 'R' and resid 306 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.289A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.909A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.632A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.010A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.524A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.680A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.103A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.750A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.553A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.506A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1242 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: 1.32 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2466 1.34 - 1.46: 1922 1.46 - 1.58: 3763 1.58 - 1.71: 0 1.71 - 1.83: 87 Bond restraints: 8238 Sorted by residual: bond pdb=" C ASP A 274 " pdb=" O ASP A 274 " ideal model delta sigma weight residual 1.236 1.217 0.019 1.15e-02 7.56e+03 2.67e+00 bond pdb=" CG LYS L 7 " pdb=" CD LYS L 7 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" C TRP L 6 " pdb=" O TRP L 6 " ideal model delta sigma weight residual 1.233 1.213 0.021 1.43e-02 4.89e+03 2.12e+00 bond pdb=" C NLE L 1 " pdb=" O NLE L 1 " ideal model delta sigma weight residual 1.231 1.257 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C ASP R 122 " pdb=" O ASP R 122 " ideal model delta sigma weight residual 1.237 1.221 0.015 1.19e-02 7.06e+03 1.64e+00 ... (remaining 8233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 10935 2.74 - 5.48: 194 5.48 - 8.22: 14 8.22 - 10.96: 2 10.96 - 13.71: 1 Bond angle restraints: 11146 Sorted by residual: angle pdb=" CA DPN L 4 " pdb=" CB DPN L 4 " pdb=" CG DPN L 4 " ideal model delta sigma weight residual 113.80 105.91 7.89 1.00e+00 1.00e+00 6.23e+01 angle pdb=" N LEU R 286 " pdb=" CA LEU R 286 " pdb=" C LEU R 286 " ideal model delta sigma weight residual 113.41 107.55 5.86 1.22e+00 6.72e-01 2.31e+01 angle pdb=" CD LYS L 7 " pdb=" CE LYS L 7 " pdb=" NZ LYS L 7 " ideal model delta sigma weight residual 111.90 98.19 13.71 3.20e+00 9.77e-02 1.83e+01 angle pdb=" N HIS L 3 " pdb=" CA HIS L 3 " pdb=" C HIS L 3 " ideal model delta sigma weight residual 111.00 100.60 10.40 2.80e+00 1.28e-01 1.38e+01 angle pdb=" N VAL R 124 " pdb=" CA VAL R 124 " pdb=" C VAL R 124 " ideal model delta sigma weight residual 110.82 114.12 -3.30 9.70e-01 1.06e+00 1.16e+01 ... (remaining 11141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4636 17.58 - 35.16: 224 35.16 - 52.74: 46 52.74 - 70.32: 21 70.32 - 87.91: 4 Dihedral angle restraints: 4931 sinusoidal: 1941 harmonic: 2990 Sorted by residual: dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -35.53 -50.47 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CA TRP R 258 " pdb=" C TRP R 258 " pdb=" N ALA R 259 " pdb=" CA ALA R 259 " ideal model delta harmonic sigma weight residual -180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CB MET R 204 " pdb=" CG MET R 204 " pdb=" SD MET R 204 " pdb=" CE MET R 204 " ideal model delta sinusoidal sigma weight residual -180.00 -126.97 -53.03 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 4928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 901 0.048 - 0.096: 275 0.096 - 0.144: 80 0.144 - 0.192: 13 0.192 - 0.240: 5 Chirality restraints: 1274 Sorted by residual: chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA HIS R 283 " pdb=" N HIS R 283 " pdb=" C HIS R 283 " pdb=" CB HIS R 283 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ARG A 385 " pdb=" N ARG A 385 " pdb=" C ARG A 385 " pdb=" CB ARG A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.56e-01 ... (remaining 1271 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 382 " 0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ILE A 382 " -0.071 2.00e-02 2.50e+03 pdb=" O ILE A 382 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE A 383 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 13 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG A 13 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG A 13 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A 14 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 377 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C ASN A 377 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN A 377 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP A 378 " -0.021 2.00e-02 2.50e+03 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 182 2.69 - 3.24: 7839 3.24 - 3.79: 12584 3.79 - 4.35: 17183 4.35 - 4.90: 28739 Nonbonded interactions: 66527 Sorted by model distance: nonbonded pdb=" O ASP A 284 " pdb=" OD1 ASP A 284 " model vdw 2.132 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.216 3.040 nonbonded pdb=" OG SER R 58 " pdb=" OG SER R 94 " model vdw 2.244 3.040 nonbonded pdb=" OG SER R 116 " pdb=" N PHE R 117 " model vdw 2.259 3.120 nonbonded pdb=" OE2 GLU R 100 " pdb="CA CA R 601 " model vdw 2.263 2.510 ... (remaining 66522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.060 Find NCS groups from input model: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 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 : 0.005 0.184 8244 Z= 0.301 Angle : 0.906 13.706 11157 Z= 0.552 Chirality : 0.052 0.240 1274 Planarity : 0.007 0.041 1414 Dihedral : 11.820 87.906 2978 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.90 % Favored : 98.00 % Rotamer: Outliers : 0.34 % Allowed : 2.49 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1002 helix: 0.96 (0.23), residues: 411 sheet: 0.82 (0.34), residues: 224 loop : 0.70 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG N 98 TYR 0.016 0.002 TYR A 339 PHE 0.025 0.002 PHE B 199 TRP 0.033 0.003 TRP B 99 HIS 0.008 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8238) covalent geometry : angle 0.90134 (11146) SS BOND : bond 0.00834 ( 4) SS BOND : angle 3.27304 ( 8) hydrogen bonds : bond 0.13795 ( 440) hydrogen bonds : angle 6.25104 ( 1242) Misc. bond : bond 0.18379 ( 1) link_TRANS : bond 0.00185 ( 1) link_TRANS : angle 1.59621 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8157 (mtmt) REVERT: A 218 ASN cc_start: 0.8357 (m-40) cc_final: 0.7774 (p0) REVERT: A 339 TYR cc_start: 0.7782 (m-80) cc_final: 0.7566 (m-80) REVERT: B 16 ASN cc_start: 0.6976 (m-40) cc_final: 0.6619 (t0) REVERT: B 37 ILE cc_start: 0.8693 (mm) cc_final: 0.8351 (pt) REVERT: B 111 TYR cc_start: 0.6769 (m-80) cc_final: 0.6294 (m-80) REVERT: B 146 LEU cc_start: 0.8304 (tp) cc_final: 0.7901 (mp) REVERT: B 217 MET cc_start: 0.6154 (ttt) cc_final: 0.5647 (mmm) REVERT: G 13 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7749 (ptt180) REVERT: G 21 MET cc_start: 0.8380 (mtm) cc_final: 0.8124 (ptp) REVERT: R 185 ILE cc_start: 0.8444 (mm) cc_final: 0.7920 (mm) REVERT: R 200 MET cc_start: 0.5703 (mtt) cc_final: 0.5181 (mtp) REVERT: R 258 TRP cc_start: 0.6863 (m100) cc_final: 0.6480 (m100) REVERT: R 316 ILE cc_start: 0.8349 (mt) cc_final: 0.7607 (mm) outliers start: 3 outliers final: 2 residues processed: 263 average time/residue: 0.1151 time to fit residues: 38.3411 Evaluate side-chains 169 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 59 GLN A 390 GLN B 32 GLN B 176 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.190245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.141606 restraints weight = 8557.524| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.02 r_work: 0.3804 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 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 8244 Z= 0.148 Angle : 0.570 5.725 11157 Z= 0.317 Chirality : 0.042 0.143 1274 Planarity : 0.004 0.043 1414 Dihedral : 4.637 51.474 1121 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.60 % Allowed : 10.85 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.26), residues: 1002 helix: 2.22 (0.24), residues: 412 sheet: 0.89 (0.33), residues: 229 loop : 0.59 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 5 TYR 0.021 0.002 TYR A 311 PHE 0.030 0.002 PHE B 235 TRP 0.018 0.002 TRP B 169 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8238) covalent geometry : angle 0.56963 (11146) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.65560 ( 8) hydrogen bonds : bond 0.05217 ( 440) hydrogen bonds : angle 4.50636 ( 1242) Misc. bond : bond 0.00071 ( 1) link_TRANS : bond 0.00083 ( 1) link_TRANS : angle 1.22408 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8517 (pp20) cc_final: 0.8286 (pp20) REVERT: A 216 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8199 (mtmt) REVERT: A 339 TYR cc_start: 0.7757 (m-80) cc_final: 0.7262 (m-80) REVERT: A 342 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7639 (ttt180) REVERT: B 37 ILE cc_start: 0.8457 (mm) cc_final: 0.8093 (pt) REVERT: B 111 TYR cc_start: 0.7085 (m-80) cc_final: 0.6559 (m-80) REVERT: B 146 LEU cc_start: 0.8435 (tp) cc_final: 0.7985 (mp) REVERT: B 217 MET cc_start: 0.6671 (ttt) cc_final: 0.5758 (mmm) REVERT: B 219 ARG cc_start: 0.7692 (mmt180) cc_final: 0.7485 (ttm110) REVERT: B 262 MET cc_start: 0.8599 (tpp) cc_final: 0.8283 (tpp) REVERT: B 325 MET cc_start: 0.8340 (mmt) cc_final: 0.7843 (mmt) REVERT: G 13 ARG cc_start: 0.8503 (ttm110) cc_final: 0.7897 (mtt90) REVERT: G 21 MET cc_start: 0.8636 (mtm) cc_final: 0.8243 (ptp) REVERT: N 98 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7557 (ttp80) REVERT: R 200 MET cc_start: 0.5933 (mtt) cc_final: 0.5659 (mtp) REVERT: R 204 MET cc_start: 0.6136 (mmm) cc_final: 0.5765 (mmt) REVERT: R 220 ARG cc_start: 0.6540 (mmt90) cc_final: 0.6164 (ttm-80) REVERT: L 5 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7657 (ttm-80) outliers start: 23 outliers final: 17 residues processed: 205 average time/residue: 0.1050 time to fit residues: 27.7985 Evaluate side-chains 178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 3.9990 chunk 61 optimal weight: 0.0020 chunk 37 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 239 ASN A 267 GLN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.187377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.138996 restraints weight = 8630.660| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.06 r_work: 0.3774 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8244 Z= 0.129 Angle : 0.517 5.424 11157 Z= 0.286 Chirality : 0.041 0.146 1274 Planarity : 0.004 0.037 1414 Dihedral : 4.189 29.212 1119 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.94 % Allowed : 11.86 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.26), residues: 1002 helix: 2.37 (0.24), residues: 412 sheet: 0.83 (0.32), residues: 232 loop : 0.45 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.014 0.001 TYR R 187 PHE 0.021 0.002 PHE B 235 TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8238) covalent geometry : angle 0.51681 (11146) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.44641 ( 8) hydrogen bonds : bond 0.04519 ( 440) hydrogen bonds : angle 4.14476 ( 1242) Misc. bond : bond 0.00007 ( 1) link_TRANS : bond 0.00079 ( 1) link_TRANS : angle 1.06714 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7871 (tttt) cc_final: 0.7301 (mptt) REVERT: A 220 HIS cc_start: 0.7449 (t-170) cc_final: 0.7011 (t-170) REVERT: A 342 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7566 (ttt90) REVERT: A 343 ASP cc_start: 0.7925 (m-30) cc_final: 0.7306 (p0) REVERT: A 347 ARG cc_start: 0.6806 (ptp90) cc_final: 0.6342 (ptp90) REVERT: B 13 GLN cc_start: 0.7964 (tp40) cc_final: 0.7707 (mm-40) REVERT: B 19 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6761 (mpt180) REVERT: B 111 TYR cc_start: 0.6907 (m-80) cc_final: 0.6334 (m-80) REVERT: B 146 LEU cc_start: 0.8592 (tp) cc_final: 0.8136 (mp) REVERT: B 163 ASP cc_start: 0.6867 (p0) cc_final: 0.6595 (p0) REVERT: B 175 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7222 (mt0) REVERT: B 217 MET cc_start: 0.6871 (ttt) cc_final: 0.6506 (ptm) REVERT: B 262 MET cc_start: 0.8629 (tpp) cc_final: 0.8132 (tpp) REVERT: B 325 MET cc_start: 0.8188 (mmt) cc_final: 0.7926 (mmt) REVERT: N 98 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7527 (ttp80) REVERT: R 200 MET cc_start: 0.6139 (mtt) cc_final: 0.5812 (mtp) REVERT: R 204 MET cc_start: 0.6133 (mmm) cc_final: 0.5727 (mmt) REVERT: R 220 ARG cc_start: 0.6510 (mmt90) cc_final: 0.6079 (ttm-80) outliers start: 26 outliers final: 20 residues processed: 185 average time/residue: 0.0993 time to fit residues: 24.0133 Evaluate side-chains 171 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 267 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.186633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137973 restraints weight = 8779.662| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.04 r_work: 0.3764 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8244 Z= 0.129 Angle : 0.521 7.790 11157 Z= 0.284 Chirality : 0.041 0.144 1274 Planarity : 0.004 0.037 1414 Dihedral : 4.147 27.477 1119 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.39 % Allowed : 13.22 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1002 helix: 2.27 (0.24), residues: 412 sheet: 0.77 (0.33), residues: 232 loop : 0.35 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 105 TYR 0.013 0.001 TYR R 187 PHE 0.018 0.002 PHE N 68 TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8238) covalent geometry : angle 0.52121 (11146) SS BOND : bond 0.00263 ( 4) SS BOND : angle 0.49508 ( 8) hydrogen bonds : bond 0.04366 ( 440) hydrogen bonds : angle 4.02843 ( 1242) Misc. bond : bond 0.00016 ( 1) link_TRANS : bond 0.00107 ( 1) link_TRANS : angle 0.98989 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7859 (tttt) cc_final: 0.7297 (mptt) REVERT: A 343 ASP cc_start: 0.7936 (m-30) cc_final: 0.7615 (p0) REVERT: B 19 ARG cc_start: 0.7019 (ttp-110) cc_final: 0.6683 (mpt180) REVERT: B 59 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6491 (t80) REVERT: B 111 TYR cc_start: 0.6819 (m-80) cc_final: 0.6358 (m-80) REVERT: B 146 LEU cc_start: 0.8704 (tp) cc_final: 0.8180 (mp) REVERT: B 217 MET cc_start: 0.7056 (ttt) cc_final: 0.6796 (ptm) REVERT: B 262 MET cc_start: 0.8574 (tpp) cc_final: 0.8237 (tpp) REVERT: B 325 MET cc_start: 0.8195 (mmt) cc_final: 0.7883 (mmt) REVERT: N 98 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7567 (ttp80) REVERT: R 71 LYS cc_start: 0.6222 (OUTLIER) cc_final: 0.5781 (ttpt) REVERT: R 220 ARG cc_start: 0.6347 (mmt90) cc_final: 0.5811 (ttm-80) REVERT: R 314 LYS cc_start: 0.7412 (pttp) cc_final: 0.6753 (ptmt) REVERT: L 5 ARG cc_start: 0.8069 (tpp80) cc_final: 0.7818 (tpp80) outliers start: 30 outliers final: 24 residues processed: 180 average time/residue: 0.1162 time to fit residues: 26.9041 Evaluate side-chains 178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.178534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.133386 restraints weight = 8982.646| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.02 r_work: 0.3672 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8244 Z= 0.206 Angle : 0.593 7.134 11157 Z= 0.325 Chirality : 0.044 0.144 1274 Planarity : 0.004 0.036 1414 Dihedral : 4.552 28.872 1119 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.97 % Allowed : 12.99 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 1002 helix: 1.97 (0.25), residues: 415 sheet: 0.57 (0.34), residues: 220 loop : -0.06 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 105 TYR 0.019 0.002 TYR R 157 PHE 0.020 0.002 PHE B 199 TRP 0.017 0.002 TRP A 234 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 8238) covalent geometry : angle 0.59313 (11146) SS BOND : bond 0.00305 ( 4) SS BOND : angle 0.66344 ( 8) hydrogen bonds : bond 0.05189 ( 440) hydrogen bonds : angle 4.26155 ( 1242) Misc. bond : bond 0.00021 ( 1) link_TRANS : bond 0.00344 ( 1) link_TRANS : angle 1.29084 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7766 (tttt) cc_final: 0.7187 (mptt) REVERT: A 209 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7193 (mt-10) REVERT: B 19 ARG cc_start: 0.7063 (ttp-110) cc_final: 0.6822 (mpt180) REVERT: B 59 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6682 (t80) REVERT: B 98 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8251 (t) REVERT: B 146 LEU cc_start: 0.8831 (tp) cc_final: 0.8354 (mp) REVERT: B 212 ASP cc_start: 0.7458 (t0) cc_final: 0.7092 (t70) REVERT: B 217 MET cc_start: 0.6935 (ttt) cc_final: 0.6574 (ptm) REVERT: B 303 ASP cc_start: 0.8053 (m-30) cc_final: 0.7785 (m-30) REVERT: B 325 MET cc_start: 0.8305 (mmt) cc_final: 0.7863 (mmt) REVERT: N 73 ASP cc_start: 0.8199 (t0) cc_final: 0.7915 (t0) REVERT: R 71 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5818 (tttt) REVERT: R 72 ASN cc_start: 0.8343 (t0) cc_final: 0.8095 (t0) REVERT: R 93 VAL cc_start: 0.4630 (OUTLIER) cc_final: 0.3959 (t) REVERT: R 220 ARG cc_start: 0.6407 (mmt90) cc_final: 0.6036 (ttm-80) REVERT: R 225 ARG cc_start: 0.7229 (mtp180) cc_final: 0.6659 (mtp-110) REVERT: R 314 LYS cc_start: 0.7377 (pttp) cc_final: 0.6671 (ptmt) outliers start: 44 outliers final: 35 residues processed: 194 average time/residue: 0.1031 time to fit residues: 26.1577 Evaluate side-chains 196 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 371 ASN A 390 GLN B 9 GLN R 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.179810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.133041 restraints weight = 9027.988| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.05 r_work: 0.3723 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8244 Z= 0.120 Angle : 0.505 6.247 11157 Z= 0.277 Chirality : 0.041 0.133 1274 Planarity : 0.004 0.052 1414 Dihedral : 4.229 25.940 1119 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.50 % Allowed : 14.80 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.27), residues: 1002 helix: 2.27 (0.25), residues: 414 sheet: 0.51 (0.33), residues: 231 loop : 0.02 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.017 0.001 TYR N 117 PHE 0.016 0.002 PHE B 199 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8238) covalent geometry : angle 0.50493 (11146) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.57785 ( 8) hydrogen bonds : bond 0.04284 ( 440) hydrogen bonds : angle 3.95740 ( 1242) Misc. bond : bond 0.00018 ( 1) link_TRANS : bond 0.00036 ( 1) link_TRANS : angle 0.87113 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7659 (tttt) cc_final: 0.7048 (mptt) REVERT: A 209 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6996 (mt-10) REVERT: B 9 GLN cc_start: 0.8279 (tp-100) cc_final: 0.7899 (tp-100) REVERT: B 19 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.6781 (mpt180) REVERT: B 59 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6648 (t80) REVERT: B 98 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8258 (t) REVERT: B 146 LEU cc_start: 0.8698 (tp) cc_final: 0.8104 (mp) REVERT: B 175 GLN cc_start: 0.8109 (tp40) cc_final: 0.7765 (mt0) REVERT: B 212 ASP cc_start: 0.7342 (t0) cc_final: 0.7010 (t0) REVERT: B 217 MET cc_start: 0.6626 (ttt) cc_final: 0.6247 (ptm) REVERT: B 325 MET cc_start: 0.8233 (mmt) cc_final: 0.7824 (mmt) REVERT: R 71 LYS cc_start: 0.6090 (mtmm) cc_final: 0.5721 (mptt) REVERT: R 93 VAL cc_start: 0.4133 (OUTLIER) cc_final: 0.3500 (t) REVERT: R 220 ARG cc_start: 0.6262 (mmt90) cc_final: 0.5838 (ttm-80) REVERT: R 225 ARG cc_start: 0.6998 (mtp180) cc_final: 0.6428 (mtp-110) REVERT: R 314 LYS cc_start: 0.7244 (pttp) cc_final: 0.6695 (ptmt) REVERT: L 5 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7416 (tpp80) outliers start: 31 outliers final: 25 residues processed: 180 average time/residue: 0.1047 time to fit residues: 24.6816 Evaluate side-chains 185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.180916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.133948 restraints weight = 9121.203| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.05 r_work: 0.3730 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8244 Z= 0.116 Angle : 0.498 6.355 11157 Z= 0.272 Chirality : 0.041 0.134 1274 Planarity : 0.004 0.041 1414 Dihedral : 4.074 25.722 1119 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.29 % Allowed : 14.46 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.27), residues: 1002 helix: 2.39 (0.25), residues: 414 sheet: 0.56 (0.33), residues: 227 loop : 0.00 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.014 0.001 TYR N 117 PHE 0.015 0.001 PHE B 199 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8238) covalent geometry : angle 0.49731 (11146) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.54515 ( 8) hydrogen bonds : bond 0.04119 ( 440) hydrogen bonds : angle 3.90199 ( 1242) Misc. bond : bond 0.00013 ( 1) link_TRANS : bond 0.00106 ( 1) link_TRANS : angle 0.95782 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7672 (tttt) cc_final: 0.7076 (mptt) REVERT: A 339 TYR cc_start: 0.7647 (m-80) cc_final: 0.6952 (m-80) REVERT: B 19 ARG cc_start: 0.7042 (ttp-110) cc_final: 0.6788 (mpt180) REVERT: B 59 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6673 (t80) REVERT: B 98 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8226 (t) REVERT: B 146 LEU cc_start: 0.8651 (tp) cc_final: 0.8066 (mp) REVERT: B 175 GLN cc_start: 0.8084 (tp40) cc_final: 0.7808 (mt0) REVERT: B 212 ASP cc_start: 0.7343 (t0) cc_final: 0.7020 (t0) REVERT: B 217 MET cc_start: 0.6721 (ttt) cc_final: 0.6281 (ptm) REVERT: N 98 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7376 (ttp80) REVERT: R 71 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5695 (mptt) REVERT: R 93 VAL cc_start: 0.4083 (OUTLIER) cc_final: 0.3450 (t) REVERT: R 220 ARG cc_start: 0.6254 (mmt90) cc_final: 0.5861 (ttm-80) REVERT: R 225 ARG cc_start: 0.6967 (mtp180) cc_final: 0.6417 (mtp-110) REVERT: R 288 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7236 (mp) REVERT: R 314 LYS cc_start: 0.7251 (pttp) cc_final: 0.6701 (ptmt) outliers start: 38 outliers final: 29 residues processed: 185 average time/residue: 0.1071 time to fit residues: 25.6385 Evaluate side-chains 195 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 20.0000 chunk 61 optimal weight: 0.0570 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.183068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.136361 restraints weight = 8955.881| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.03 r_work: 0.3752 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8244 Z= 0.104 Angle : 0.498 7.581 11157 Z= 0.269 Chirality : 0.041 0.135 1274 Planarity : 0.004 0.038 1414 Dihedral : 3.996 23.653 1119 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.62 % Allowed : 16.05 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.27), residues: 1002 helix: 2.61 (0.25), residues: 409 sheet: 0.60 (0.34), residues: 227 loop : 0.03 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.012 0.001 TYR N 117 PHE 0.014 0.001 PHE B 241 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8238) covalent geometry : angle 0.49798 (11146) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.51876 ( 8) hydrogen bonds : bond 0.03880 ( 440) hydrogen bonds : angle 3.86851 ( 1242) Misc. bond : bond 0.00025 ( 1) link_TRANS : bond 0.00085 ( 1) link_TRANS : angle 0.71567 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7716 (tttt) cc_final: 0.7129 (mptt) REVERT: A 339 TYR cc_start: 0.7687 (m-80) cc_final: 0.7042 (m-80) REVERT: B 9 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7759 (tp-100) REVERT: B 19 ARG cc_start: 0.7108 (ttp-110) cc_final: 0.6852 (mpt180) REVERT: B 59 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6656 (t80) REVERT: B 98 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8243 (t) REVERT: B 146 LEU cc_start: 0.8622 (tp) cc_final: 0.8178 (mt) REVERT: B 175 GLN cc_start: 0.8046 (tp40) cc_final: 0.7820 (mt0) REVERT: B 212 ASP cc_start: 0.7250 (t0) cc_final: 0.6944 (t0) REVERT: B 217 MET cc_start: 0.6719 (ttt) cc_final: 0.6314 (ptm) REVERT: N 39 GLN cc_start: 0.7866 (tp40) cc_final: 0.7636 (tt0) REVERT: N 46 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7307 (mm-30) REVERT: N 98 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7446 (ttp80) REVERT: R 71 LYS cc_start: 0.6037 (OUTLIER) cc_final: 0.5719 (mptt) REVERT: R 220 ARG cc_start: 0.6105 (mmt90) cc_final: 0.5760 (ttm-80) REVERT: R 225 ARG cc_start: 0.7009 (mtp180) cc_final: 0.6482 (mtp-110) REVERT: R 288 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7220 (mp) REVERT: R 314 LYS cc_start: 0.7242 (pttp) cc_final: 0.6665 (ptmt) outliers start: 32 outliers final: 23 residues processed: 181 average time/residue: 0.1094 time to fit residues: 25.7135 Evaluate side-chains 184 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 59 GLN A 239 ASN A 390 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.181633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.134481 restraints weight = 9059.144| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 3.03 r_work: 0.3746 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8244 Z= 0.118 Angle : 0.521 8.966 11157 Z= 0.278 Chirality : 0.041 0.135 1274 Planarity : 0.004 0.037 1414 Dihedral : 3.995 25.050 1119 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.84 % Allowed : 16.27 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.27), residues: 1002 helix: 2.55 (0.25), residues: 409 sheet: 0.58 (0.34), residues: 227 loop : 0.01 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 5 TYR 0.012 0.001 TYR R 187 PHE 0.014 0.001 PHE B 199 TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8238) covalent geometry : angle 0.52069 (11146) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.52652 ( 8) hydrogen bonds : bond 0.04026 ( 440) hydrogen bonds : angle 3.91657 ( 1242) Misc. bond : bond 0.00012 ( 1) link_TRANS : bond 0.00150 ( 1) link_TRANS : angle 0.96112 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8352 (pp20) cc_final: 0.8122 (pp20) REVERT: A 28 LYS cc_start: 0.7704 (tttt) cc_final: 0.7101 (mptt) REVERT: A 339 TYR cc_start: 0.7662 (m-80) cc_final: 0.7006 (m-80) REVERT: B 9 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7771 (tp-100) REVERT: B 19 ARG cc_start: 0.7176 (ttp-110) cc_final: 0.6913 (mpt180) REVERT: B 59 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6697 (t80) REVERT: B 98 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8151 (t) REVERT: B 146 LEU cc_start: 0.8659 (tp) cc_final: 0.8106 (mp) REVERT: B 175 GLN cc_start: 0.8028 (tp40) cc_final: 0.7810 (mt0) REVERT: B 212 ASP cc_start: 0.7293 (t0) cc_final: 0.6958 (t0) REVERT: B 217 MET cc_start: 0.6710 (ttt) cc_final: 0.6281 (ptm) REVERT: N 32 TYR cc_start: 0.8597 (m-80) cc_final: 0.8259 (m-80) REVERT: N 39 GLN cc_start: 0.7875 (tp40) cc_final: 0.7651 (tt0) REVERT: N 43 LYS cc_start: 0.7882 (mttt) cc_final: 0.7485 (mttm) REVERT: N 46 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7098 (mm-30) REVERT: N 98 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7468 (ttp80) REVERT: R 71 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5507 (tttt) REVERT: R 93 VAL cc_start: 0.3878 (OUTLIER) cc_final: 0.3234 (t) REVERT: R 220 ARG cc_start: 0.6331 (mmt90) cc_final: 0.5951 (ttm-80) REVERT: R 225 ARG cc_start: 0.7002 (mtp180) cc_final: 0.6427 (mtp-110) REVERT: R 314 LYS cc_start: 0.7248 (pttp) cc_final: 0.6665 (ptmt) outliers start: 34 outliers final: 28 residues processed: 188 average time/residue: 0.1069 time to fit residues: 26.1041 Evaluate side-chains 197 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 9.9990 chunk 24 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.180206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.132863 restraints weight = 9117.650| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.06 r_work: 0.3721 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8244 Z= 0.146 Angle : 0.564 10.053 11157 Z= 0.302 Chirality : 0.043 0.136 1274 Planarity : 0.004 0.037 1414 Dihedral : 4.165 25.568 1119 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.07 % Allowed : 16.50 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.27), residues: 1002 helix: 2.46 (0.25), residues: 409 sheet: 0.48 (0.34), residues: 219 loop : -0.06 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 5 TYR 0.013 0.001 TYR A 339 PHE 0.016 0.002 PHE B 199 TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8238) covalent geometry : angle 0.56338 (11146) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.51012 ( 8) hydrogen bonds : bond 0.04325 ( 440) hydrogen bonds : angle 4.02874 ( 1242) Misc. bond : bond 0.00000 ( 1) link_TRANS : bond 0.00237 ( 1) link_TRANS : angle 1.08558 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7686 (tttt) cc_final: 0.7094 (mptt) REVERT: A 339 TYR cc_start: 0.7643 (m-80) cc_final: 0.6979 (m-80) REVERT: B 9 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7780 (tp-100) REVERT: B 19 ARG cc_start: 0.7148 (ttp-110) cc_final: 0.6899 (mpt180) REVERT: B 98 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8167 (t) REVERT: B 146 LEU cc_start: 0.8727 (tp) cc_final: 0.8187 (mp) REVERT: B 175 GLN cc_start: 0.8022 (tp40) cc_final: 0.7800 (mt0) REVERT: B 212 ASP cc_start: 0.7403 (t0) cc_final: 0.7042 (t0) REVERT: B 217 MET cc_start: 0.6474 (ttt) cc_final: 0.5836 (ptm) REVERT: N 43 LYS cc_start: 0.7940 (mttt) cc_final: 0.7650 (mttm) REVERT: N 46 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7131 (mm-30) REVERT: N 98 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7593 (ttp80) REVERT: R 71 LYS cc_start: 0.5886 (OUTLIER) cc_final: 0.5526 (tttt) REVERT: R 93 VAL cc_start: 0.3896 (OUTLIER) cc_final: 0.3253 (t) REVERT: R 220 ARG cc_start: 0.6285 (mmt90) cc_final: 0.5901 (ttm-80) REVERT: R 225 ARG cc_start: 0.6970 (mtp180) cc_final: 0.6404 (mtp-110) REVERT: R 314 LYS cc_start: 0.7274 (pttp) cc_final: 0.6688 (ptmt) outliers start: 36 outliers final: 33 residues processed: 177 average time/residue: 0.1116 time to fit residues: 25.5863 Evaluate side-chains 200 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 79 MET Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN R 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.179000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134473 restraints weight = 9161.969| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.95 r_work: 0.3705 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8244 Z= 0.153 Angle : 0.574 10.888 11157 Z= 0.307 Chirality : 0.043 0.137 1274 Planarity : 0.004 0.036 1414 Dihedral : 4.226 25.819 1119 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.29 % Allowed : 16.61 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.27), residues: 1002 helix: 2.37 (0.25), residues: 409 sheet: 0.34 (0.33), residues: 229 loop : -0.06 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 5 TYR 0.014 0.002 TYR A 339 PHE 0.016 0.002 PHE B 199 TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8238) covalent geometry : angle 0.57376 (11146) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.60170 ( 8) hydrogen bonds : bond 0.04514 ( 440) hydrogen bonds : angle 4.07310 ( 1242) Misc. bond : bond 0.00004 ( 1) link_TRANS : bond 0.00247 ( 1) link_TRANS : angle 1.13548 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.08 seconds wall clock time: 40 minutes 35.42 seconds (2435.42 seconds total)