Starting phenix.real_space_refine on Fri Sep 11 03:13:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ld3_23280/09_2026/7ld3_23280.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ld3_23280/09_2026/7ld3_23280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ld3_23280/09_2026/7ld3_23280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ld3_23280/09_2026/7ld3_23280.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ld3_23280/09_2026/7ld3_23280.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ld3_23280/09_2026/7ld3_23280.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ld3_23280/09_2026/7ld3_23280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ld3_23280/09_2026/7ld3_23280.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 53 5.16 5 Cl 1 4.86 5 C 4498 2.51 5 N 1189 2.21 5 O 1269 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7016 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1693 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 207} Chain breaks: 2 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2273 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 14, 'TRANS': 273} Chain breaks: 1 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2568 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'ADN%rna3p': 1, 'XTD': 1} Classifications: {'undetermined': 2, 'water': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Time building chain proxies: 1.57, per 1000 atoms: 0.22 Number of scatterers: 7016 At special positions: 0 Unit cell: (127.204, 88.382, 102.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 53 16.00 F 6 9.00 O 1269 8.00 N 1189 7.00 C 4498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 80 " - pdb=" SG CYS R 169 " distance=2.03 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 263 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 380.4 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 47.1% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.702A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.671A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.834A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 216 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.105A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.526A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.644A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 353 removed outlier: 3.704A pdb=" N ASN A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 36 removed outlier: 3.715A pdb=" N ALA R 10 " --> pdb=" O SER R 6 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA R 11 " --> pdb=" O ALA R 7 " (cutoff:3.500A) Proline residue: R 25 - end of helix Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 62 through 72 Processing helix chain 'R' and resid 77 through 111 Proline residue: R 86 - end of helix Processing helix chain 'R' and resid 120 through 140 Processing helix chain 'R' and resid 141 through 144 Processing helix chain 'R' and resid 148 through 160 Processing helix chain 'R' and resid 170 through 175 removed outlier: 3.664A pdb=" N VAL R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 183 Processing helix chain 'R' and resid 184 through 189 Processing helix chain 'R' and resid 189 through 211 Processing helix chain 'R' and resid 225 through 260 Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 266 through 279 removed outlier: 3.731A pdb=" N THR R 270 " --> pdb=" O PRO R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 288 removed outlier: 3.664A pdb=" N VAL R 287 " --> pdb=" O MET R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 300 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.593A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.778A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 8.921A pdb=" N ALA A 221 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 74 through 76 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.586A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.590A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.027A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.648A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.521A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.497A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.773A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1080 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: 0.99 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1636 1.33 - 1.45: 1604 1.45 - 1.58: 3841 1.58 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 7159 Sorted by residual: bond pdb=" C VAL R 24 " pdb=" N PRO R 25 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.69e+00 bond pdb=" CA ILE G 28 " pdb=" CB ILE G 28 " ideal model delta sigma weight residual 1.547 1.577 -0.030 1.68e-02 3.54e+03 3.29e+00 bond pdb=" C XTD R 402 " pdb=" C7 XTD R 402 " ideal model delta sigma weight residual 1.448 1.483 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.92e+00 bond pdb=" CB PRO R 142 " pdb=" CG PRO R 142 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.80e+00 ... (remaining 7154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 9458 2.73 - 5.45: 205 5.45 - 8.18: 32 8.18 - 10.91: 7 10.91 - 13.64: 2 Bond angle restraints: 9704 Sorted by residual: angle pdb=" CA CYS R 263 " pdb=" CB CYS R 263 " pdb=" SG CYS R 263 " ideal model delta sigma weight residual 114.40 124.77 -10.37 2.30e+00 1.89e-01 2.03e+01 angle pdb=" CA ILE G 28 " pdb=" CB ILE G 28 " pdb=" CG2 ILE G 28 " ideal model delta sigma weight residual 110.50 117.83 -7.33 1.70e+00 3.46e-01 1.86e+01 angle pdb=" CA CYS R 260 " pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " ideal model delta sigma weight residual 114.40 123.83 -9.43 2.30e+00 1.89e-01 1.68e+01 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 129.94 -13.64 3.50e+00 8.16e-02 1.52e+01 angle pdb=" CA LYS G 29 " pdb=" CB LYS G 29 " pdb=" CG LYS G 29 " ideal model delta sigma weight residual 114.10 106.36 7.74 2.00e+00 2.50e-01 1.50e+01 ... (remaining 9699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3884 16.42 - 32.84: 299 32.84 - 49.26: 71 49.26 - 65.68: 9 65.68 - 82.11: 4 Dihedral angle restraints: 4267 sinusoidal: 1677 harmonic: 2590 Sorted by residual: dihedral pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -43.23 -42.77 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLN R 74 " pdb=" C GLN R 74 " pdb=" N THR R 75 " pdb=" CA THR R 75 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1028 0.112 - 0.224: 88 0.224 - 0.337: 1 0.337 - 0.449: 0 0.449 - 0.561: 1 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CB ILE G 9 " pdb=" CA ILE G 9 " pdb=" CG1 ILE G 9 " pdb=" CG2 ILE G 9 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE G 28 " pdb=" CA ILE G 28 " pdb=" CG1 ILE G 28 " pdb=" CG2 ILE G 28 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1115 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 XTD R 402 " -0.047 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" C11 XTD R 402 " 0.023 2.00e-02 2.50e+03 pdb=" C12 XTD R 402 " 0.029 2.00e-02 2.50e+03 pdb=" C13 XTD R 402 " 0.015 2.00e-02 2.50e+03 pdb=" C14 XTD R 402 " -0.037 2.00e-02 2.50e+03 pdb=" C15 XTD R 402 " 0.014 2.00e-02 2.50e+03 pdb=" C16 XTD R 402 " 0.013 2.00e-02 2.50e+03 pdb=" C17 XTD R 402 " -0.035 2.00e-02 2.50e+03 pdb=" C18 XTD R 402 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADN R 401 " -0.059 2.00e-02 2.50e+03 2.45e-02 1.65e+01 pdb=" C2 ADN R 401 " 0.008 2.00e-02 2.50e+03 pdb=" C4 ADN R 401 " 0.016 2.00e-02 2.50e+03 pdb=" C5 ADN R 401 " 0.012 2.00e-02 2.50e+03 pdb=" C6 ADN R 401 " -0.010 2.00e-02 2.50e+03 pdb=" C8 ADN R 401 " 0.020 2.00e-02 2.50e+03 pdb=" N1 ADN R 401 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ADN R 401 " 0.022 2.00e-02 2.50e+03 pdb=" N6 ADN R 401 " -0.035 2.00e-02 2.50e+03 pdb=" N7 ADN R 401 " 0.016 2.00e-02 2.50e+03 pdb=" N9 ADN R 401 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 173 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C THR B 173 " 0.063 2.00e-02 2.50e+03 pdb=" O THR B 173 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY B 174 " -0.022 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1769 2.80 - 3.33: 6327 3.33 - 3.85: 11784 3.85 - 4.38: 14139 4.38 - 4.90: 24289 Nonbonded interactions: 58308 Sorted by model distance: nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.277 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.295 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.312 3.040 nonbonded pdb=" O VAL R 138 " pdb=" OH TYR R 179 " model vdw 2.319 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.322 3.040 ... (remaining 58303 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: 1.130 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.470 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.006 0.084 7161 Z= 0.270 Angle : 1.020 13.637 9708 Z= 0.567 Chirality : 0.063 0.561 1118 Planarity : 0.008 0.087 1211 Dihedral : 12.702 82.106 2577 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.25), residues: 872 helix: -1.42 (0.22), residues: 404 sheet: 0.84 (0.38), residues: 173 loop : -1.24 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 13 TYR 0.033 0.003 TYR A 297 PHE 0.042 0.003 PHE R 275 TRP 0.024 0.003 TRP B 99 HIS 0.006 0.002 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.27 ( 7159) covalent geometry : angle 1.01842 / 0.57 ( 9704) SS BOND : bond 0.00756 / 0.37 ( 2) SS BOND : angle 3.04824 / 1.79 ( 4) hydrogen bonds : bond 0.22409 / 15.22 ( 374) hydrogen bonds : angle 7.74790 / 5.43 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8398 (m-80) cc_final: 0.7763 (m-80) REVERT: B 259 GLN cc_start: 0.8285 (pt0) cc_final: 0.7913 (pt0) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.0865 time to fit residues: 14.0323 Evaluate side-chains 76 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN A 332 ASN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134668 restraints weight = 7667.739| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.59 r_work: 0.3353 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7161 Z= 0.182 Angle : 0.609 8.147 9708 Z= 0.328 Chirality : 0.043 0.162 1118 Planarity : 0.005 0.066 1211 Dihedral : 5.966 32.592 969 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.06 % Allowed : 9.11 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.27), residues: 872 helix: 0.20 (0.25), residues: 417 sheet: 0.48 (0.37), residues: 178 loop : -0.82 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 8 TYR 0.010 0.001 TYR B 124 PHE 0.032 0.002 PHE R 275 TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 7159) covalent geometry : angle 0.60783 / 0.33 ( 9704) SS BOND : bond 0.00412 / 0.20 ( 2) SS BOND : angle 1.85728 / 1.10 ( 4) hydrogen bonds : bond 0.04271 / 2.86 ( 374) hydrogen bonds : angle 4.97277 / 3.46 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.272 Fit side-chains REVERT: A 32 ARG cc_start: 0.8114 (ptt-90) cc_final: 0.7847 (ptp-170) REVERT: A 51 LYS cc_start: 0.8862 (mptt) cc_final: 0.8661 (mptt) REVERT: A 208 GLU cc_start: 0.7900 (pt0) cc_final: 0.7659 (pt0) REVERT: A 210 LYS cc_start: 0.9287 (ptmt) cc_final: 0.8999 (pttt) REVERT: B 101 MET cc_start: 0.8913 (mtp) cc_final: 0.8650 (mtp) REVERT: B 146 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8192 (mp) outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.0886 time to fit residues: 11.2222 Evaluate side-chains 83 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130898 restraints weight = 7589.869| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.63 r_work: 0.3320 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7161 Z= 0.185 Angle : 0.566 7.221 9708 Z= 0.304 Chirality : 0.044 0.161 1118 Planarity : 0.005 0.057 1211 Dihedral : 5.241 32.697 969 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.38 % Allowed : 10.30 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.28), residues: 872 helix: 0.72 (0.26), residues: 411 sheet: 0.15 (0.35), residues: 179 loop : -0.80 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 108 TYR 0.017 0.001 TYR B 111 PHE 0.029 0.002 PHE R 275 TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 7159) covalent geometry : angle 0.56469 / 0.30 ( 9704) SS BOND : bond 0.00446 / 0.21 ( 2) SS BOND : angle 1.85034 / 1.10 ( 4) hydrogen bonds : bond 0.03964 / 2.66 ( 374) hydrogen bonds : angle 4.74841 / 3.34 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.275 Fit side-chains REVERT: A 208 GLU cc_start: 0.8017 (pt0) cc_final: 0.7739 (pt0) REVERT: A 210 LYS cc_start: 0.9266 (ptmt) cc_final: 0.8846 (pttt) REVERT: R 29 LEU cc_start: 0.7624 (mp) cc_final: 0.7386 (mp) REVERT: B 146 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8247 (mp) outliers start: 18 outliers final: 10 residues processed: 91 average time/residue: 0.0853 time to fit residues: 10.5756 Evaluate side-chains 83 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.165394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133135 restraints weight = 7672.794| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.55 r_work: 0.3345 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7161 Z= 0.151 Angle : 0.531 6.912 9708 Z= 0.284 Chirality : 0.042 0.155 1118 Planarity : 0.004 0.051 1211 Dihedral : 4.898 32.609 969 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.25 % Allowed : 11.76 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.29), residues: 872 helix: 1.04 (0.27), residues: 411 sheet: -0.07 (0.36), residues: 176 loop : -0.73 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 108 TYR 0.015 0.001 TYR B 111 PHE 0.028 0.001 PHE R 275 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7159) covalent geometry : angle 0.53023 / 0.28 ( 9704) SS BOND : bond 0.00418 / 0.20 ( 2) SS BOND : angle 1.75718 / 1.04 ( 4) hydrogen bonds : bond 0.03543 / 2.37 ( 374) hydrogen bonds : angle 4.58183 / 3.23 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.265 Fit side-chains REVERT: A 210 LYS cc_start: 0.9286 (ptmt) cc_final: 0.8950 (ptmt) REVERT: B 197 ARG cc_start: 0.8327 (mtp85) cc_final: 0.8125 (mtp85) outliers start: 17 outliers final: 13 residues processed: 86 average time/residue: 0.0897 time to fit residues: 10.4430 Evaluate side-chains 83 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.2980 chunk 6 optimal weight: 0.0470 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.168097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136817 restraints weight = 7648.274| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.61 r_work: 0.3380 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7161 Z= 0.103 Angle : 0.502 6.722 9708 Z= 0.269 Chirality : 0.040 0.147 1118 Planarity : 0.004 0.046 1211 Dihedral : 4.654 32.246 969 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 11.89 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.29), residues: 872 helix: 1.34 (0.27), residues: 409 sheet: 0.01 (0.37), residues: 176 loop : -0.68 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.012 0.001 TYR B 111 PHE 0.027 0.001 PHE R 275 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 7159) covalent geometry : angle 0.50090 / 0.27 ( 9704) SS BOND : bond 0.00349 / 0.17 ( 2) SS BOND : angle 1.78313 / 1.05 ( 4) hydrogen bonds : bond 0.03106 / 2.08 ( 374) hydrogen bonds : angle 4.35522 / 3.07 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.273 Fit side-chains REVERT: A 208 GLU cc_start: 0.7977 (pt0) cc_final: 0.7674 (pt0) REVERT: B 55 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8513 (mt) REVERT: B 197 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8128 (mtp85) outliers start: 18 outliers final: 12 residues processed: 89 average time/residue: 0.0880 time to fit residues: 10.6845 Evaluate side-chains 83 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.166038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133654 restraints weight = 7692.596| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.60 r_work: 0.3353 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7161 Z= 0.135 Angle : 0.511 6.667 9708 Z= 0.273 Chirality : 0.042 0.149 1118 Planarity : 0.004 0.046 1211 Dihedral : 4.615 32.663 969 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.25 % Allowed : 12.81 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.29), residues: 872 helix: 1.34 (0.27), residues: 413 sheet: 0.01 (0.37), residues: 175 loop : -0.77 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 108 TYR 0.011 0.001 TYR B 111 PHE 0.026 0.001 PHE R 275 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7159) covalent geometry : angle 0.50964 / 0.27 ( 9704) SS BOND : bond 0.00394 / 0.19 ( 2) SS BOND : angle 1.70300 / 1.01 ( 4) hydrogen bonds : bond 0.03230 / 2.16 ( 374) hydrogen bonds : angle 4.34703 / 3.08 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.264 Fit side-chains REVERT: A 208 GLU cc_start: 0.7981 (pt0) cc_final: 0.7655 (pt0) REVERT: A 210 LYS cc_start: 0.9149 (pttm) cc_final: 0.8925 (pttp) REVERT: B 55 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8465 (mt) outliers start: 17 outliers final: 13 residues processed: 88 average time/residue: 0.0831 time to fit residues: 10.1249 Evaluate side-chains 83 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 7 optimal weight: 0.0270 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.167785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135627 restraints weight = 7592.807| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.55 r_work: 0.3375 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7161 Z= 0.108 Angle : 0.509 8.115 9708 Z= 0.267 Chirality : 0.041 0.142 1118 Planarity : 0.004 0.044 1211 Dihedral : 4.637 34.628 969 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.51 % Allowed : 12.95 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.29), residues: 872 helix: 1.54 (0.27), residues: 411 sheet: 0.14 (0.38), residues: 173 loop : -0.72 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 108 TYR 0.010 0.001 TYR B 264 PHE 0.026 0.001 PHE R 275 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7159) covalent geometry : angle 0.50790 / 0.27 ( 9704) SS BOND : bond 0.00350 / 0.17 ( 2) SS BOND : angle 1.71184 / 1.01 ( 4) hydrogen bonds : bond 0.03041 / 2.03 ( 374) hydrogen bonds : angle 4.25505 / 3.01 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.323 Fit side-chains REVERT: A 277 GLU cc_start: 0.7495 (tp30) cc_final: 0.7230 (tp30) REVERT: B 55 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8414 (mt) outliers start: 19 outliers final: 12 residues processed: 84 average time/residue: 0.0871 time to fit residues: 10.0875 Evaluate side-chains 77 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN R 92 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.168838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138257 restraints weight = 7680.104| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.69 r_work: 0.3361 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7161 Z= 0.106 Angle : 0.504 7.698 9708 Z= 0.265 Chirality : 0.040 0.138 1118 Planarity : 0.004 0.044 1211 Dihedral : 4.543 35.284 969 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 13.21 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.29), residues: 872 helix: 1.62 (0.27), residues: 413 sheet: 0.19 (0.38), residues: 173 loop : -0.73 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.012 0.001 TYR B 111 PHE 0.025 0.001 PHE R 275 TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7159) covalent geometry : angle 0.50273 / 0.26 ( 9704) SS BOND : bond 0.00354 / 0.17 ( 2) SS BOND : angle 1.66423 / 0.98 ( 4) hydrogen bonds : bond 0.02962 / 1.97 ( 374) hydrogen bonds : angle 4.18747 / 2.96 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.274 Fit side-chains REVERT: A 51 LYS cc_start: 0.8871 (mptt) cc_final: 0.8609 (mmtt) REVERT: A 277 GLU cc_start: 0.7611 (tp30) cc_final: 0.7312 (tp30) REVERT: A 290 GLU cc_start: 0.7511 (pm20) cc_final: 0.6995 (pm20) REVERT: B 55 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8367 (mt) REVERT: B 164 THR cc_start: 0.8366 (p) cc_final: 0.8045 (p) REVERT: B 262 MET cc_start: 0.8544 (ttm) cc_final: 0.7993 (ttm) outliers start: 18 outliers final: 13 residues processed: 84 average time/residue: 0.0784 time to fit residues: 9.2083 Evaluate side-chains 81 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 0.0030 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 47 optimal weight: 0.0370 chunk 53 optimal weight: 0.4980 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.169700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.136183 restraints weight = 7617.535| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.66 r_work: 0.3382 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7161 Z= 0.103 Angle : 0.547 14.177 9708 Z= 0.280 Chirality : 0.040 0.144 1118 Planarity : 0.004 0.043 1211 Dihedral : 4.594 36.221 969 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.25 % Allowed : 13.47 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.29), residues: 872 helix: 1.73 (0.27), residues: 413 sheet: 0.23 (0.38), residues: 173 loop : -0.71 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.007 0.001 TYR B 264 PHE 0.024 0.001 PHE R 275 TRP 0.021 0.001 TRP B 169 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 7159) covalent geometry : angle 0.53670 / 0.28 ( 9704) SS BOND : bond 0.00795 / 0.38 ( 2) SS BOND : angle 5.21866 / 2.46 ( 4) hydrogen bonds : bond 0.02921 / 1.95 ( 374) hydrogen bonds : angle 4.17828 / 2.95 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 277 GLU cc_start: 0.7627 (tp30) cc_final: 0.7305 (tp30) REVERT: A 290 GLU cc_start: 0.7564 (pm20) cc_final: 0.7103 (pm20) REVERT: B 55 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8370 (mt) REVERT: B 164 THR cc_start: 0.8300 (p) cc_final: 0.7971 (p) outliers start: 17 outliers final: 11 residues processed: 87 average time/residue: 0.0767 time to fit residues: 9.3553 Evaluate side-chains 82 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136313 restraints weight = 7693.859| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.58 r_work: 0.3361 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7161 Z= 0.131 Angle : 0.564 13.928 9708 Z= 0.290 Chirality : 0.042 0.134 1118 Planarity : 0.004 0.044 1211 Dihedral : 4.627 36.477 969 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.98 % Allowed : 14.00 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 872 helix: 1.68 (0.27), residues: 413 sheet: 0.07 (0.37), residues: 178 loop : -0.65 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.012 0.001 TYR B 111 PHE 0.023 0.001 PHE R 275 TRP 0.020 0.001 TRP B 169 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7159) covalent geometry : angle 0.55313 / 0.29 ( 9704) SS BOND : bond 0.00693 / 0.33 ( 2) SS BOND : angle 5.33410 / 2.47 ( 4) hydrogen bonds : bond 0.03095 / 2.04 ( 374) hydrogen bonds : angle 4.24797 / 3.01 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8834 (mptt) cc_final: 0.8626 (mmtt) REVERT: A 277 GLU cc_start: 0.7693 (tp30) cc_final: 0.7435 (tp30) REVERT: A 290 GLU cc_start: 0.7566 (pm20) cc_final: 0.7058 (pm20) REVERT: A 307 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7987 (mtpp) REVERT: R 143 MET cc_start: 0.7956 (mtm) cc_final: 0.7703 (mtp) REVERT: B 55 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8296 (mt) REVERT: B 164 THR cc_start: 0.8386 (p) cc_final: 0.8074 (p) outliers start: 15 outliers final: 12 residues processed: 82 average time/residue: 0.0815 time to fit residues: 9.3527 Evaluate side-chains 82 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 0.0060 chunk 66 optimal weight: 6.9990 chunk 63 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.169631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139104 restraints weight = 7659.060| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.61 r_work: 0.3386 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7161 Z= 0.105 Angle : 0.541 12.514 9708 Z= 0.277 Chirality : 0.040 0.135 1118 Planarity : 0.004 0.043 1211 Dihedral : 4.588 36.717 969 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.98 % Allowed : 14.13 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.30), residues: 872 helix: 1.78 (0.27), residues: 413 sheet: 0.08 (0.37), residues: 178 loop : -0.62 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.008 0.001 TYR B 264 PHE 0.024 0.001 PHE R 275 TRP 0.021 0.001 TRP B 169 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7159) covalent geometry : angle 0.53005 / 0.27 ( 9704) SS BOND : bond 0.00517 / 0.25 ( 2) SS BOND : angle 5.25150 / 2.51 ( 4) hydrogen bonds : bond 0.02899 / 1.92 ( 374) hydrogen bonds : angle 4.15861 / 2.93 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.48 seconds wall clock time: 36 minutes 1.88 seconds (2161.88 seconds total)