Starting phenix.real_space_refine on Wed Mar 12 17:24:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f55_31458/03_2025/7f55_31458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f55_31458/03_2025/7f55_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_2025/7f55_31458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f55_31458/03_2025/7f55_31458.map" model { file = "/net/cci-nas-00/data/ceres_data/7f55_31458/03_2025/7f55_31458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f55_31458/03_2025/7f55_31458.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.89, per 1000 atoms: 0.60 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: 2.19 Conformation dependent library (CDL) restraints added in 925.3 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: 0.84 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: 2.47 Time building geometry restraints manager: 2.57 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: 0.630 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.820 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.370 ------------------------------------------------------------------------------- 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 : 0.004 0.047 8238 Z= 0.290 Angle : 0.901 13.706 11146 Z= 0.551 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.003 TRP B 99 HIS 0.008 0.002 HIS B 183 PHE 0.025 0.002 PHE B 199 TYR 0.016 0.002 TYR A 339 ARG 0.023 0.002 ARG N 98 *********************** 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 : 0.844 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: 0.7867 (mm) REVERT: R 200 MET cc_start: 0.5703 (mtt) cc_final: 0.5180 (mtp) REVERT: R 258 TRP cc_start: 0.6863 (m100) cc_final: 0.6481 (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: 0.2637 time to fit residues: 87.2670 Evaluate side-chains 170 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 83 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- 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 = 0.4422 r_free = 0.4422 target = 0.190970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.141847 restraints weight = 8533.381| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.10 r_work: 0.3806 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8238 Z= 0.206 Angle : 0.564 5.689 11146 Z= 0.314 Chirality : 0.042 0.144 1274 Planarity : 0.004 0.042 1414 Dihedral : 4.651 51.484 1121 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.71 % Allowed : 10.62 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS R 264 PHE 0.027 0.002 PHE B 235 TYR 0.017 0.002 TYR A 311 ARG 0.007 0.001 ARG L 5 *********************** 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 212 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8191 (mtmt) REVERT: A 339 TYR cc_start: 0.7760 (m-80) cc_final: 0.7306 (m-80) REVERT: A 342 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7527 (ttt180) REVERT: A 343 ASP cc_start: 0.8010 (m-30) cc_final: 0.7759 (p0) REVERT: B 37 ILE cc_start: 0.8444 (mm) cc_final: 0.8070 (pt) REVERT: B 111 TYR cc_start: 0.7099 (m-80) cc_final: 0.6536 (m-80) REVERT: B 146 LEU cc_start: 0.8427 (tp) cc_final: 0.7960 (mp) REVERT: B 217 MET cc_start: 0.6681 (ttt) cc_final: 0.5962 (mmm) REVERT: G 21 MET cc_start: 0.8638 (mtm) cc_final: 0.8191 (ptp) REVERT: N 43 LYS cc_start: 0.7537 (mttt) cc_final: 0.7268 (mttt) REVERT: N 98 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7547 (ttp80) REVERT: R 200 MET cc_start: 0.5923 (mtt) cc_final: 0.5647 (mtp) REVERT: R 204 MET cc_start: 0.6256 (mmm) cc_final: 0.5918 (mmt) REVERT: R 220 ARG cc_start: 0.6572 (mmt90) cc_final: 0.6280 (ttm-80) outliers start: 24 outliers final: 16 residues processed: 203 average time/residue: 0.2416 time to fit residues: 63.4601 Evaluate side-chains 183 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 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 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 = 0.4378 r_free = 0.4378 target = 0.186162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.137346 restraints weight = 8847.743| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.11 r_work: 0.3755 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8238 Z= 0.193 Angle : 0.521 5.376 11146 Z= 0.288 Chirality : 0.042 0.159 1274 Planarity : 0.004 0.037 1414 Dihedral : 4.204 27.424 1119 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.94 % Allowed : 11.75 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.26), residues: 1002 helix: 2.32 (0.24), residues: 413 sheet: 0.78 (0.32), residues: 233 loop : 0.44 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS R 264 PHE 0.021 0.002 PHE B 235 TYR 0.014 0.002 TYR R 187 ARG 0.007 0.000 ARG N 105 *********************** 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 203 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7821 (tttt) cc_final: 0.7588 (ttmm) REVERT: A 220 HIS cc_start: 0.7441 (t-170) cc_final: 0.7223 (t-170) REVERT: A 229 ASP cc_start: 0.7360 (m-30) cc_final: 0.7132 (m-30) REVERT: A 342 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7567 (ttt180) REVERT: A 347 ARG cc_start: 0.6848 (ptp90) cc_final: 0.6430 (ptp-170) REVERT: B 13 GLN cc_start: 0.7981 (tp40) cc_final: 0.7778 (mm-40) REVERT: B 19 ARG cc_start: 0.7069 (ttp-110) cc_final: 0.6714 (mpt180) REVERT: B 111 TYR cc_start: 0.6871 (m-80) cc_final: 0.6334 (m-80) REVERT: B 146 LEU cc_start: 0.8633 (tp) cc_final: 0.8279 (mt) REVERT: B 175 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7293 (mt0) REVERT: B 217 MET cc_start: 0.6887 (ttt) cc_final: 0.6255 (ptm) REVERT: B 228 ASP cc_start: 0.7593 (m-30) cc_final: 0.7339 (m-30) REVERT: B 325 MET cc_start: 0.8221 (mmt) cc_final: 0.7937 (mmt) REVERT: G 22 GLU cc_start: 0.6029 (mt-10) cc_final: 0.5668 (mp0) REVERT: N 98 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7520 (ttp80) REVERT: R 71 LYS cc_start: 0.6220 (mtmm) cc_final: 0.5817 (tttt) REVERT: R 218 MET cc_start: 0.8029 (tpp) cc_final: 0.7763 (tpp) REVERT: R 220 ARG cc_start: 0.6447 (mmt90) cc_final: 0.6089 (ttm-80) outliers start: 26 outliers final: 20 residues processed: 191 average time/residue: 0.2449 time to fit residues: 60.0350 Evaluate side-chains 173 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain B residue 98 SER 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 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 16 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 A 292 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.185979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.140044 restraints weight = 8653.779| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.00 r_work: 0.3752 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8238 Z= 0.202 Angle : 0.520 6.173 11146 Z= 0.285 Chirality : 0.041 0.141 1274 Planarity : 0.004 0.037 1414 Dihedral : 4.161 27.870 1119 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.82 % Allowed : 14.69 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.27), residues: 1002 helix: 2.28 (0.24), residues: 413 sheet: 0.69 (0.33), residues: 237 loop : 0.35 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS R 264 PHE 0.017 0.002 PHE B 235 TYR 0.013 0.001 TYR R 187 ARG 0.006 0.000 ARG N 105 *********************** 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 192 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7915 (tttt) cc_final: 0.7324 (mptt) REVERT: A 229 ASP cc_start: 0.7389 (m-30) cc_final: 0.7186 (m-30) REVERT: A 342 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.7573 (ttt90) REVERT: A 343 ASP cc_start: 0.8003 (m-30) cc_final: 0.7579 (p0) REVERT: B 19 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6715 (mpt180) REVERT: B 59 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6467 (t80) REVERT: B 111 TYR cc_start: 0.6840 (m-80) cc_final: 0.6367 (m-80) REVERT: B 146 LEU cc_start: 0.8704 (tp) cc_final: 0.8299 (mt) REVERT: B 212 ASP cc_start: 0.7393 (t0) cc_final: 0.6998 (t0) REVERT: B 217 MET cc_start: 0.7166 (ttt) cc_final: 0.6663 (ptm) REVERT: B 325 MET cc_start: 0.8285 (mmt) cc_final: 0.7876 (mmt) REVERT: G 22 GLU cc_start: 0.6080 (mt-10) cc_final: 0.5779 (mp0) REVERT: N 98 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7614 (ttp80) REVERT: R 71 LYS cc_start: 0.6252 (mtmm) cc_final: 0.5858 (tttt) REVERT: R 220 ARG cc_start: 0.6429 (mmt90) cc_final: 0.5869 (ttm-80) REVERT: R 225 ARG cc_start: 0.7273 (mtp180) cc_final: 0.6740 (mtp-110) REVERT: R 314 LYS cc_start: 0.7237 (pttp) cc_final: 0.6539 (ptmt) outliers start: 25 outliers final: 21 residues processed: 180 average time/residue: 0.2606 time to fit residues: 60.1493 Evaluate side-chains 178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL 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 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 16 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 292 ASN A 371 ASN A 390 GLN B 9 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.183287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.138689 restraints weight = 8719.330| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.94 r_work: 0.3745 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8238 Z= 0.192 Angle : 0.510 7.387 11146 Z= 0.277 Chirality : 0.041 0.137 1274 Planarity : 0.004 0.037 1414 Dihedral : 4.128 26.925 1119 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.07 % Allowed : 14.01 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 1002 helix: 2.29 (0.25), residues: 415 sheet: 0.63 (0.33), residues: 236 loop : 0.22 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.005 0.001 HIS R 264 PHE 0.015 0.002 PHE B 199 TYR 0.011 0.001 TYR A 339 ARG 0.011 0.001 ARG N 105 *********************** 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 209 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7849 (tttt) cc_final: 0.7269 (mptt) REVERT: A 342 ARG cc_start: 0.7803 (ttp-170) cc_final: 0.7564 (ttt90) REVERT: A 343 ASP cc_start: 0.7982 (m-30) cc_final: 0.7642 (p0) REVERT: B 9 GLN cc_start: 0.8255 (tp-100) cc_final: 0.8020 (tp-100) REVERT: B 19 ARG cc_start: 0.7074 (ttp-110) cc_final: 0.6780 (mpt180) REVERT: B 59 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.6512 (t80) REVERT: B 146 LEU cc_start: 0.8703 (tp) cc_final: 0.8283 (mt) REVERT: B 175 GLN cc_start: 0.8026 (tp40) cc_final: 0.7740 (mt0) REVERT: B 212 ASP cc_start: 0.7500 (t0) cc_final: 0.7116 (t0) REVERT: B 217 MET cc_start: 0.6934 (ttt) cc_final: 0.6592 (ptm) REVERT: B 325 MET cc_start: 0.8279 (mmt) cc_final: 0.7801 (mmt) REVERT: G 22 GLU cc_start: 0.6056 (mt-10) cc_final: 0.5797 (mp0) REVERT: N 73 ASP cc_start: 0.8267 (t0) cc_final: 0.8029 (t0) REVERT: R 71 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5865 (tttt) REVERT: R 93 VAL cc_start: 0.4429 (OUTLIER) cc_final: 0.3755 (t) REVERT: R 220 ARG cc_start: 0.6429 (mmt90) cc_final: 0.5950 (ttm-80) REVERT: R 225 ARG cc_start: 0.7251 (mtp180) cc_final: 0.6727 (mtp-110) outliers start: 36 outliers final: 30 residues processed: 190 average time/residue: 0.2391 time to fit residues: 59.1152 Evaluate side-chains 196 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 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 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 9 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 A 292 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.176462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132290 restraints weight = 9158.448| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.11 r_work: 0.3661 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8238 Z= 0.283 Angle : 0.563 6.361 11146 Z= 0.309 Chirality : 0.043 0.136 1274 Planarity : 0.004 0.068 1414 Dihedral : 4.414 27.955 1119 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.31 % Allowed : 13.79 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.27), residues: 1002 helix: 2.19 (0.25), residues: 408 sheet: 0.51 (0.34), residues: 220 loop : -0.01 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS R 264 PHE 0.018 0.002 PHE B 199 TYR 0.016 0.002 TYR R 157 ARG 0.005 0.000 ARG B 134 *********************** 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 218 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7736 (tttt) cc_final: 0.7137 (mptt) REVERT: A 342 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7573 (ttt90) REVERT: A 343 ASP cc_start: 0.8003 (m-30) cc_final: 0.7517 (p0) REVERT: A 347 ARG cc_start: 0.6700 (ptp-110) cc_final: 0.6470 (ptp90) REVERT: B 9 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7944 (tp-100) REVERT: B 19 ARG cc_start: 0.7090 (ttp-110) cc_final: 0.6834 (mpt180) REVERT: B 59 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6694 (t80) REVERT: B 98 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8279 (t) REVERT: B 212 ASP cc_start: 0.7549 (t0) cc_final: 0.7116 (t0) REVERT: B 217 MET cc_start: 0.6857 (ttt) cc_final: 0.6269 (ptm) REVERT: B 234 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: B 303 ASP cc_start: 0.7980 (m-30) cc_final: 0.7710 (m-30) REVERT: B 325 MET cc_start: 0.8275 (mmt) cc_final: 0.7833 (mmt) REVERT: G 41 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6886 (p) REVERT: G 47 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8638 (tm-30) REVERT: N 73 ASP cc_start: 0.8216 (t0) cc_final: 0.7996 (t0) REVERT: R 71 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5728 (tttt) REVERT: R 93 VAL cc_start: 0.4280 (OUTLIER) cc_final: 0.3592 (t) REVERT: R 220 ARG cc_start: 0.6446 (mmt90) cc_final: 0.6050 (ttm-80) REVERT: R 314 LYS cc_start: 0.7200 (pttp) cc_final: 0.6575 (ptmt) outliers start: 47 outliers final: 35 residues processed: 196 average time/residue: 0.2329 time to fit residues: 59.3370 Evaluate side-chains 204 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 300 LYS Chi-restraints excluded: chain A residue 309 GLU 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 234 PHE 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 R residue 312 THR 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 82 optimal weight: 0.1980 chunk 46 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 292 ASN A 390 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.178494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134234 restraints weight = 9142.849| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.02 r_work: 0.3695 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8238 Z= 0.210 Angle : 0.525 6.479 11146 Z= 0.287 Chirality : 0.042 0.137 1274 Planarity : 0.004 0.050 1414 Dihedral : 4.290 26.497 1119 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.63 % Allowed : 15.37 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 1002 helix: 2.18 (0.25), residues: 414 sheet: 0.40 (0.34), residues: 221 loop : 0.02 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS R 264 PHE 0.016 0.002 PHE B 199 TYR 0.014 0.002 TYR B 264 ARG 0.006 0.000 ARG B 134 *********************** 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 214 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7743 (tttt) cc_final: 0.7125 (mptt) REVERT: A 339 TYR cc_start: 0.7686 (m-80) cc_final: 0.6897 (m-80) REVERT: A 342 ARG cc_start: 0.7909 (ttp-170) cc_final: 0.7610 (ttt180) REVERT: A 343 ASP cc_start: 0.8060 (m-30) cc_final: 0.7573 (p0) REVERT: A 347 ARG cc_start: 0.6798 (ptp-110) cc_final: 0.6462 (ptp90) REVERT: B 9 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7920 (tp-100) REVERT: B 19 ARG cc_start: 0.7113 (ttp-110) cc_final: 0.6878 (mpt180) REVERT: B 59 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6767 (t80) REVERT: B 98 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8252 (t) REVERT: B 175 GLN cc_start: 0.8123 (tp40) cc_final: 0.7851 (mt0) REVERT: B 188 MET cc_start: 0.7166 (mmp) cc_final: 0.6903 (mmp) REVERT: B 212 ASP cc_start: 0.7590 (t0) cc_final: 0.7167 (t0) REVERT: B 217 MET cc_start: 0.6803 (ttt) cc_final: 0.6386 (ptm) REVERT: B 234 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: B 303 ASP cc_start: 0.7974 (m-30) cc_final: 0.7689 (m-30) REVERT: B 325 MET cc_start: 0.8255 (mmt) cc_final: 0.7869 (mmt) REVERT: G 47 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8623 (tm-30) REVERT: N 73 ASP cc_start: 0.8176 (t0) cc_final: 0.7921 (t0) REVERT: R 71 LYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5764 (mptt) REVERT: R 93 VAL cc_start: 0.4172 (OUTLIER) cc_final: 0.3498 (t) REVERT: R 220 ARG cc_start: 0.6348 (mmt90) cc_final: 0.5962 (ttm-80) REVERT: R 225 ARG cc_start: 0.7413 (mtp180) cc_final: 0.6787 (mtp-110) REVERT: R 288 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7393 (mp) REVERT: R 314 LYS cc_start: 0.7237 (pttp) cc_final: 0.6642 (ptmt) outliers start: 41 outliers final: 32 residues processed: 194 average time/residue: 0.2898 time to fit residues: 72.7835 Evaluate side-chains 203 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 309 GLU 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 234 PHE 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 288 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 390 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.177930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133530 restraints weight = 9233.621| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.13 r_work: 0.3679 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8238 Z= 0.228 Angle : 0.537 6.557 11146 Z= 0.294 Chirality : 0.042 0.137 1274 Planarity : 0.004 0.040 1414 Dihedral : 4.331 26.308 1119 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.86 % Allowed : 16.61 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 1002 helix: 2.26 (0.25), residues: 408 sheet: 0.43 (0.34), residues: 215 loop : -0.11 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS R 264 PHE 0.016 0.002 PHE B 199 TYR 0.013 0.002 TYR A 339 ARG 0.009 0.000 ARG L 5 *********************** 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 213 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7721 (tttt) cc_final: 0.7116 (mptt) REVERT: A 339 TYR cc_start: 0.7736 (m-80) cc_final: 0.6938 (m-80) REVERT: A 342 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7591 (ttt180) REVERT: A 343 ASP cc_start: 0.8073 (m-30) cc_final: 0.7738 (p0) REVERT: B 9 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7930 (tp-100) REVERT: B 19 ARG cc_start: 0.7104 (ttp-110) cc_final: 0.6879 (mpt180) REVERT: B 59 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6814 (t80) REVERT: B 98 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8283 (t) REVERT: B 175 GLN cc_start: 0.8108 (tp40) cc_final: 0.7845 (mt0) REVERT: B 212 ASP cc_start: 0.7491 (t0) cc_final: 0.7096 (t0) REVERT: B 234 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: B 303 ASP cc_start: 0.7951 (m-30) cc_final: 0.7667 (m-30) REVERT: G 47 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8611 (tm-30) REVERT: N 46 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7273 (mm-30) REVERT: N 73 ASP cc_start: 0.8043 (t0) cc_final: 0.7813 (t0) REVERT: N 98 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7579 (ttp80) REVERT: R 93 VAL cc_start: 0.4243 (OUTLIER) cc_final: 0.3565 (t) REVERT: R 220 ARG cc_start: 0.6429 (mmt90) cc_final: 0.5985 (ttm-80) REVERT: R 225 ARG cc_start: 0.7365 (mtp180) cc_final: 0.6720 (mtp-110) REVERT: R 288 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7357 (mp) outliers start: 43 outliers final: 33 residues processed: 193 average time/residue: 0.2681 time to fit residues: 67.3035 Evaluate side-chains 198 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain A residue 309 GLU 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 234 PHE Chi-restraints excluded: chain B residue 250 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 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 A 292 ASN A 390 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.177958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.134689 restraints weight = 9338.032| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.00 r_work: 0.3688 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8238 Z= 0.226 Angle : 0.547 6.729 11146 Z= 0.298 Chirality : 0.042 0.138 1274 Planarity : 0.004 0.038 1414 Dihedral : 4.300 26.311 1119 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.20 % Allowed : 16.50 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 1002 helix: 2.26 (0.25), residues: 408 sheet: 0.41 (0.34), residues: 215 loop : -0.16 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS R 264 PHE 0.016 0.002 PHE B 199 TYR 0.013 0.002 TYR A 339 ARG 0.009 0.000 ARG L 5 *********************** 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 210 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7736 (tttt) cc_final: 0.7135 (mptt) REVERT: A 339 TYR cc_start: 0.7727 (m-80) cc_final: 0.6807 (m-80) REVERT: B 9 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7813 (tp40) REVERT: B 13 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7996 (mm-40) REVERT: B 19 ARG cc_start: 0.7047 (ttp-110) cc_final: 0.6807 (mpt180) REVERT: B 59 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6842 (t80) REVERT: B 98 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8282 (t) REVERT: B 175 GLN cc_start: 0.8048 (tp40) cc_final: 0.7803 (mt0) REVERT: B 212 ASP cc_start: 0.7525 (t0) cc_final: 0.7140 (t0) REVERT: B 234 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: B 303 ASP cc_start: 0.7842 (m-30) cc_final: 0.7545 (m-30) REVERT: G 19 LEU cc_start: 0.7110 (mp) cc_final: 0.6836 (mp) REVERT: G 47 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8623 (tm-30) REVERT: N 46 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7174 (mm-30) REVERT: N 73 ASP cc_start: 0.8085 (t0) cc_final: 0.7792 (t0) REVERT: R 71 LYS cc_start: 0.5951 (mptt) cc_final: 0.4607 (tttt) REVERT: R 93 VAL cc_start: 0.4140 (OUTLIER) cc_final: 0.3462 (t) REVERT: R 225 ARG cc_start: 0.7370 (mtp180) cc_final: 0.6732 (mtp-110) REVERT: R 288 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7455 (mp) REVERT: R 314 LYS cc_start: 0.7250 (pttp) cc_final: 0.6598 (ptmt) outliers start: 46 outliers final: 37 residues processed: 188 average time/residue: 0.2444 time to fit residues: 59.4198 Evaluate side-chains 200 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 213 GLN 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 275 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 309 GLU 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 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 274 THR 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 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 213 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 390 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.175963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.131602 restraints weight = 9217.904| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.10 r_work: 0.3651 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8238 Z= 0.292 Angle : 0.598 6.877 11146 Z= 0.325 Chirality : 0.044 0.138 1274 Planarity : 0.004 0.041 1414 Dihedral : 4.513 26.794 1119 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.31 % Allowed : 16.50 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 1002 helix: 2.00 (0.25), residues: 414 sheet: 0.25 (0.33), residues: 225 loop : -0.26 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.004 0.001 HIS R 264 PHE 0.017 0.002 PHE B 199 TYR 0.016 0.002 TYR A 339 ARG 0.009 0.001 ARG L 5 ********************** 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 213 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7795 (tttt) cc_final: 0.7179 (mptt) REVERT: A 339 TYR cc_start: 0.7866 (m-80) cc_final: 0.6932 (m-80) REVERT: B 9 GLN cc_start: 0.8219 (tp-100) cc_final: 0.8014 (tp40) REVERT: B 19 ARG cc_start: 0.6981 (ttp-110) cc_final: 0.6750 (mpt180) REVERT: B 98 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8260 (t) REVERT: B 175 GLN cc_start: 0.8063 (tp40) cc_final: 0.7807 (mt0) REVERT: B 212 ASP cc_start: 0.7607 (t0) cc_final: 0.7208 (t0) REVERT: B 234 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: B 303 ASP cc_start: 0.7840 (m-30) cc_final: 0.7552 (m-30) REVERT: G 19 LEU cc_start: 0.7076 (mp) cc_final: 0.6779 (mp) REVERT: G 47 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8660 (tm-30) REVERT: N 43 LYS cc_start: 0.7939 (mttt) cc_final: 0.7622 (mttm) REVERT: R 93 VAL cc_start: 0.4370 (OUTLIER) cc_final: 0.3691 (t) REVERT: R 120 ASN cc_start: 0.6960 (m-40) cc_final: 0.6706 (t0) REVERT: R 225 ARG cc_start: 0.7404 (mtp180) cc_final: 0.6722 (mtp-110) REVERT: R 288 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7517 (mp) REVERT: R 314 LYS cc_start: 0.7316 (pttp) cc_final: 0.6695 (ptmt) outliers start: 47 outliers final: 39 residues processed: 190 average time/residue: 0.2396 time to fit residues: 59.4264 Evaluate side-chains 203 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 213 GLN 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 275 SER Chi-restraints excluded: chain A residue 309 GLU 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 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 274 THR 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 N residue 117 TYR 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 213 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 292 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.182378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.138509 restraints weight = 8905.139| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.97 r_work: 0.3724 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8238 Z= 0.186 Angle : 0.557 8.900 11146 Z= 0.302 Chirality : 0.042 0.155 1274 Planarity : 0.004 0.040 1414 Dihedral : 4.275 25.184 1119 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.29 % Allowed : 17.40 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 1002 helix: 2.34 (0.25), residues: 409 sheet: 0.35 (0.33), residues: 227 loop : -0.13 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS R 264 PHE 0.016 0.002 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.010 0.001 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5404.45 seconds wall clock time: 94 minutes 48.14 seconds (5688.14 seconds total)