Starting phenix.real_space_refine on Wed Aug 5 03:51:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hdp_34677/08_2026/8hdp_34677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hdp_34677/08_2026/8hdp_34677.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/8hdp_34677/08_2026/8hdp_34677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hdp_34677/08_2026/8hdp_34677.map" model { file = "/net/cci-nas-00/data/ceres_data/8hdp_34677/08_2026/8hdp_34677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hdp_34677/08_2026/8hdp_34677.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hdp_34677/08_2026/8hdp_34677.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hdp_34677/08_2026/8hdp_34677.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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5280 2.51 5 N 1430 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8282 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1985 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 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: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2166 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {'ADN%rna3p': 1, 'CLR': 4} Classifications: {'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 2.06, per 1000 atoms: 0.25 Number of scatterers: 8282 At special positions: 0 Unit cell: (95.68, 76.96, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1519 8.00 N 1430 7.00 C 5280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 470.0 milliseconds 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 42.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 4.267A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.636A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.511A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.243A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.537A pdb=" N TYR A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.556A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.777A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.702A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.825A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 35 Processing helix chain 'R' and resid 40 through 59 Processing helix chain 'R' and resid 59 through 69 Processing helix chain 'R' and resid 74 through 109 removed outlier: 3.583A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 118 through 138 Processing helix chain 'R' and resid 138 through 144 removed outlier: 3.814A pdb=" N LEU R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 184 Processing helix chain 'R' and resid 186 through 191 Processing helix chain 'R' and resid 191 through 214 Processing helix chain 'R' and resid 225 through 260 removed outlier: 3.572A pdb=" N PHE R 243 " --> pdb=" O ILE R 239 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 267 through 291 removed outlier: 4.472A pdb=" N ASN R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER R 283 " --> pdb=" O SER R 279 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 294 through 309 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.317A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ALA A 105 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG A 42 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE A 107 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 44 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL A 109 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 46 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.605A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.965A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.891A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.651A pdb=" N CYS B 149 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER B 160 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE B 151 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 158 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.613A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.163A 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: 3.809A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.857A 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: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.784A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1448 1.33 - 1.45: 2236 1.45 - 1.57: 4701 1.57 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8458 Sorted by residual: bond pdb=" C4 ADN R 401 " pdb=" C5 ADN R 401 " ideal model delta sigma weight residual 1.385 1.467 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C5 ADN R 401 " pdb=" C6 ADN R 401 " ideal model delta sigma weight residual 1.408 1.482 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C MET R 238 " pdb=" O MET R 238 " ideal model delta sigma weight residual 1.236 1.202 0.033 1.17e-02 7.31e+03 8.14e+00 bond pdb=" N TRP R 247 " pdb=" CA TRP R 247 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.84e+00 bond pdb=" N GLU R 174 " pdb=" CA GLU R 174 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.27e-02 6.20e+03 6.58e+00 ... (remaining 8453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.13: 11482 6.13 - 12.26: 12 12.26 - 18.38: 1 18.38 - 24.51: 1 24.51 - 30.64: 2 Bond angle restraints: 11498 Sorted by residual: angle pdb=" C17 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sigma weight residual 110.18 79.54 30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C12 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sigma weight residual 111.01 81.73 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sigma weight residual 112.24 90.75 21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" C12 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C17 CLR R 404 " ideal model delta sigma weight residual 116.52 130.09 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C1' ADN R 401 " pdb=" C2' ADN R 401 " pdb=" C3' ADN R 401 " ideal model delta sigma weight residual 101.30 105.27 -3.97 1.00e+00 1.00e+00 1.58e+01 ... (remaining 11493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.89: 4894 23.89 - 47.78: 85 47.78 - 71.67: 12 71.67 - 95.56: 2 95.56 - 119.45: 1 Dihedral angle restraints: 4994 sinusoidal: 1963 harmonic: 3031 Sorted by residual: dihedral pdb=" C10 CLR R 402 " pdb=" C1 CLR R 402 " pdb=" C2 CLR R 402 " pdb=" C3 CLR R 402 " ideal model delta sinusoidal sigma weight residual -56.83 62.62 -119.45 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" N GLN R 6 " pdb=" C GLN R 6 " pdb=" CA GLN R 6 " pdb=" CB GLN R 6 " ideal model delta harmonic sigma weight residual 122.80 132.23 -9.43 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" N PHE R 173 " pdb=" C PHE R 173 " pdb=" CA PHE R 173 " pdb=" CB PHE R 173 " ideal model delta harmonic sigma weight residual 122.80 132.18 -9.38 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 4991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 1317 0.383 - 0.766: 1 0.766 - 1.149: 0 1.149 - 1.532: 0 1.532 - 1.914: 2 Chirality restraints: 1320 Sorted by residual: chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -1.02 -1.91 2.00e-01 2.50e+01 9.16e+01 chirality pdb=" CG LEU R 3 " pdb=" CB LEU R 3 " pdb=" CD1 LEU R 3 " pdb=" CD2 LEU R 3 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.20e+01 chirality pdb=" CA GLN R 6 " pdb=" N GLN R 6 " pdb=" C GLN R 6 " pdb=" CB GLN R 6 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 1317 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 237 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C ALA R 237 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA R 237 " -0.018 2.00e-02 2.50e+03 pdb=" N MET R 238 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 173 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C PHE R 173 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE R 173 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU R 174 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 178 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C PRO R 178 " -0.036 2.00e-02 2.50e+03 pdb=" O PRO R 178 " 0.014 2.00e-02 2.50e+03 pdb=" N MET R 179 " 0.012 2.00e-02 2.50e+03 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 108 2.58 - 3.16: 7464 3.16 - 3.74: 13104 3.74 - 4.32: 18541 4.32 - 4.90: 30724 Nonbonded interactions: 69941 Sorted by model distance: nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.006 3.040 nonbonded pdb=" OG SER R 235 " pdb=" NH2 ARG R 293 " model vdw 2.022 3.120 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.080 3.120 nonbonded pdb=" OD1 ASP A 111 " pdb=" OG SER A 113 " model vdw 2.114 3.040 nonbonded pdb=" OG1 THR R 40 " pdb=" OD1 ASN R 43 " model vdw 2.136 3.040 ... (remaining 69936 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.003 0.082 8461 Z= 0.192 Angle : 0.755 30.642 11504 Z= 0.343 Chirality : 0.085 1.914 1320 Planarity : 0.003 0.041 1446 Dihedral : 9.480 119.454 3025 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.57 % Allowed : 6.04 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.25), residues: 1027 helix: 0.17 (0.25), residues: 401 sheet: -2.09 (0.31), residues: 207 loop : -1.98 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.005 0.001 TYR R 10 PHE 0.014 0.001 PHE R 173 TRP 0.009 0.001 TRP R 247 HIS 0.005 0.001 HIS R 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.19 ( 8458) covalent geometry : angle 0.75535 / 0.34 (11498) SS BOND : bond 0.00149 / 0.07 ( 3) SS BOND : angle 0.35947 / 0.23 ( 6) hydrogen bonds : bond 0.12068 / 8.19 ( 436) hydrogen bonds : angle 6.25935 / 4.40 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 289 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8121 (tt) cc_final: 0.7907 (pt) REVERT: A 212 TYR cc_start: 0.8614 (m-80) cc_final: 0.7916 (m-80) REVERT: B 9 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8591 (pp30) REVERT: B 10 GLU cc_start: 0.8695 (tp30) cc_final: 0.8449 (tp30) REVERT: B 63 TRP cc_start: 0.8484 (m100) cc_final: 0.8247 (m100) REVERT: B 171 ILE cc_start: 0.6986 (mp) cc_final: 0.6612 (mm) REVERT: B 280 LYS cc_start: 0.8845 (tttm) cc_final: 0.8560 (ttpp) REVERT: B 289 TYR cc_start: 0.8423 (m-80) cc_final: 0.7747 (m-80) REVERT: B 297 TRP cc_start: 0.7497 (m100) cc_final: 0.7256 (m100) REVERT: N 60 TYR cc_start: 0.8323 (m-80) cc_final: 0.7396 (m-80) REVERT: N 87 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8048 (mtmm) REVERT: R 227 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7691 (pt0) outliers start: 5 outliers final: 1 residues processed: 293 average time/residue: 0.1145 time to fit residues: 44.1257 Evaluate side-chains 179 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 239 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN A 123 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS B 62 HIS B 91 HIS B 119 ASN B 156 GLN B 230 ASN B 295 ASN R 175 ASN R 280 HIS ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.104969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079960 restraints weight = 16990.200| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.16 r_work: 0.3177 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8461 Z= 0.198 Angle : 0.793 31.623 11504 Z= 0.360 Chirality : 0.070 1.992 1320 Planarity : 0.004 0.058 1446 Dihedral : 5.448 100.511 1175 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.31 % Allowed : 11.40 % Favored : 85.29 % 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: -0.64 (0.26), residues: 1027 helix: 1.03 (0.26), residues: 397 sheet: -1.65 (0.30), residues: 230 loop : -1.02 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.012 0.001 TYR B 59 PHE 0.018 0.002 PHE R 173 TRP 0.013 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 8458) covalent geometry : angle 0.79292 / 0.36 (11498) SS BOND : bond 0.00097 / 0.05 ( 3) SS BOND : angle 1.52390 / 0.56 ( 6) hydrogen bonds : bond 0.03448 / 2.36 ( 436) hydrogen bonds : angle 5.06316 / 3.58 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ARG cc_start: 0.8552 (ptp90) cc_final: 0.8294 (ptp90) REVERT: A 230 ASP cc_start: 0.8366 (m-30) cc_final: 0.8127 (m-30) REVERT: B 9 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8842 (pp30) REVERT: B 10 GLU cc_start: 0.8938 (tp30) cc_final: 0.8621 (tp30) REVERT: B 15 LYS cc_start: 0.9254 (ptpt) cc_final: 0.8997 (ptpp) REVERT: B 155 ASN cc_start: 0.8079 (t0) cc_final: 0.7855 (t0) REVERT: B 280 LYS cc_start: 0.9078 (tttm) cc_final: 0.8833 (ttpp) REVERT: N 32 TYR cc_start: 0.8416 (m-80) cc_final: 0.7836 (m-80) REVERT: N 36 TRP cc_start: 0.8675 (m100) cc_final: 0.8415 (m100) REVERT: N 38 ARG cc_start: 0.8089 (ptt-90) cc_final: 0.7878 (ptt90) REVERT: N 60 TYR cc_start: 0.8468 (m-80) cc_final: 0.7175 (m-80) REVERT: N 65 LYS cc_start: 0.8633 (tptm) cc_final: 0.8279 (tppp) REVERT: N 105 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7989 (mtp180) REVERT: R 227 GLN cc_start: 0.8466 (mm-40) cc_final: 0.7982 (pt0) REVERT: R 229 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7234 (tm-30) outliers start: 29 outliers final: 20 residues processed: 188 average time/residue: 0.1133 time to fit residues: 28.2192 Evaluate side-chains 158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 303 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 0.0670 chunk 100 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.102214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077552 restraints weight = 16879.280| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.04 r_work: 0.3138 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8461 Z= 0.175 Angle : 0.765 31.613 11504 Z= 0.343 Chirality : 0.068 1.947 1320 Planarity : 0.004 0.058 1446 Dihedral : 5.421 102.167 1173 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.85 % Allowed : 13.34 % Favored : 83.81 % 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 (0.26), residues: 1027 helix: 1.31 (0.26), residues: 393 sheet: -1.11 (0.33), residues: 205 loop : -0.91 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 72 TYR 0.010 0.001 TYR B 264 PHE 0.014 0.001 PHE A 74 TRP 0.012 0.002 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 8458) covalent geometry : angle 0.76436 / 0.34 (11498) SS BOND : bond 0.00211 / 0.10 ( 3) SS BOND : angle 1.17031 / 0.49 ( 6) hydrogen bonds : bond 0.03425 / 2.34 ( 436) hydrogen bonds : angle 4.87127 / 3.44 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6363 (tpp) cc_final: 0.6070 (tpp) REVERT: A 169 ARG cc_start: 0.8584 (ptp90) cc_final: 0.8266 (ptp90) REVERT: A 230 ASP cc_start: 0.8395 (m-30) cc_final: 0.8175 (m-30) REVERT: B 9 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8828 (pp30) REVERT: B 10 GLU cc_start: 0.8963 (tp30) cc_final: 0.8635 (tp30) REVERT: B 15 LYS cc_start: 0.9231 (ptpt) cc_final: 0.9008 (ptpp) REVERT: B 35 ASN cc_start: 0.8698 (m110) cc_final: 0.8451 (m-40) REVERT: B 280 LYS cc_start: 0.9092 (tttm) cc_final: 0.8615 (ttpp) REVERT: G 29 LYS cc_start: 0.8878 (tppt) cc_final: 0.8631 (tppt) REVERT: N 38 ARG cc_start: 0.8203 (ptt-90) cc_final: 0.7943 (ptt90) REVERT: N 53 GLN cc_start: 0.8770 (mp10) cc_final: 0.8293 (mp10) REVERT: N 60 TYR cc_start: 0.8648 (m-80) cc_final: 0.8333 (m-80) REVERT: R 170 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7229 (mptt) REVERT: R 177 VAL cc_start: 0.9063 (t) cc_final: 0.8730 (m) REVERT: R 227 GLN cc_start: 0.8507 (mm-40) cc_final: 0.7989 (pt0) REVERT: R 229 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7218 (tm-30) outliers start: 25 outliers final: 20 residues processed: 165 average time/residue: 0.1194 time to fit residues: 25.8039 Evaluate side-chains 154 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.102478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077987 restraints weight = 16887.313| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.98 r_work: 0.3168 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8461 Z= 0.140 Angle : 0.736 30.981 11504 Z= 0.325 Chirality : 0.067 1.944 1320 Planarity : 0.004 0.060 1446 Dihedral : 5.266 103.634 1173 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.96 % Allowed : 14.48 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.26), residues: 1027 helix: 1.49 (0.26), residues: 393 sheet: -1.03 (0.32), residues: 222 loop : -0.67 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.018 0.001 TYR R 308 PHE 0.014 0.001 PHE A 74 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 8458) covalent geometry : angle 0.73594 / 0.32 (11498) SS BOND : bond 0.00181 / 0.08 ( 3) SS BOND : angle 1.15597 / 0.49 ( 6) hydrogen bonds : bond 0.03302 / 2.26 ( 436) hydrogen bonds : angle 4.72764 / 3.35 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8052 (tt) cc_final: 0.7636 (pt) REVERT: A 169 ARG cc_start: 0.8601 (ptp90) cc_final: 0.8361 (ptp90) REVERT: A 230 ASP cc_start: 0.8367 (m-30) cc_final: 0.8143 (m-30) REVERT: B 8 ARG cc_start: 0.9101 (mmt90) cc_final: 0.8878 (mmt90) REVERT: B 9 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8782 (pp30) REVERT: B 10 GLU cc_start: 0.8938 (tp30) cc_final: 0.8581 (tp30) REVERT: B 15 LYS cc_start: 0.9228 (ptpt) cc_final: 0.9027 (ptpp) REVERT: B 35 ASN cc_start: 0.8684 (m110) cc_final: 0.8477 (m-40) REVERT: B 138 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7863 (mm-30) REVERT: B 280 LYS cc_start: 0.9095 (tttm) cc_final: 0.8610 (ttpp) REVERT: G 20 LYS cc_start: 0.9342 (mmtp) cc_final: 0.9126 (mmtp) REVERT: G 22 GLU cc_start: 0.9040 (tp30) cc_final: 0.8704 (tp30) REVERT: G 29 LYS cc_start: 0.8888 (tppt) cc_final: 0.8598 (tppt) REVERT: N 38 ARG cc_start: 0.8467 (ptt-90) cc_final: 0.8215 (ptt90) REVERT: N 53 GLN cc_start: 0.8849 (mp10) cc_final: 0.8460 (mp10) REVERT: N 60 TYR cc_start: 0.8647 (m-80) cc_final: 0.8273 (m-80) REVERT: N 80 TYR cc_start: 0.8080 (m-80) cc_final: 0.7686 (m-80) REVERT: N 82 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8140 (tp-100) REVERT: R 170 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7321 (mptt) REVERT: R 227 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8040 (pt0) REVERT: R 229 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6936 (tm-30) outliers start: 26 outliers final: 19 residues processed: 170 average time/residue: 0.1118 time to fit residues: 25.2739 Evaluate side-chains 155 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 0.0000 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.102221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078045 restraints weight = 16809.979| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.91 r_work: 0.3166 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8461 Z= 0.129 Angle : 0.713 30.791 11504 Z= 0.316 Chirality : 0.067 1.936 1320 Planarity : 0.004 0.059 1446 Dihedral : 5.319 105.562 1173 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.42 % Allowed : 14.94 % Favored : 81.64 % 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: 0.32 (0.26), residues: 1027 helix: 1.66 (0.26), residues: 391 sheet: -0.81 (0.32), residues: 222 loop : -0.51 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.011 0.001 TYR A 170 PHE 0.015 0.001 PHE A 74 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8458) covalent geometry : angle 0.71276 / 0.32 (11498) SS BOND : bond 0.00117 / 0.05 ( 3) SS BOND : angle 0.78727 / 0.35 ( 6) hydrogen bonds : bond 0.03292 / 2.23 ( 436) hydrogen bonds : angle 4.65060 / 3.31 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.5654 (tpt) cc_final: 0.5052 (mmm) REVERT: A 62 ILE cc_start: 0.8121 (tt) cc_final: 0.7631 (pt) REVERT: A 169 ARG cc_start: 0.8599 (ptp90) cc_final: 0.8347 (ptp90) REVERT: A 230 ASP cc_start: 0.8391 (m-30) cc_final: 0.8168 (m-30) REVERT: B 8 ARG cc_start: 0.9161 (mmt90) cc_final: 0.8936 (mmt90) REVERT: B 9 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8817 (pp30) REVERT: B 10 GLU cc_start: 0.8929 (tp30) cc_final: 0.8604 (tp30) REVERT: B 35 ASN cc_start: 0.8827 (m110) cc_final: 0.8492 (m-40) REVERT: G 20 LYS cc_start: 0.9357 (mmtp) cc_final: 0.9144 (mmtp) REVERT: G 22 GLU cc_start: 0.9063 (tp30) cc_final: 0.8818 (tp30) REVERT: G 29 LYS cc_start: 0.8912 (tppt) cc_final: 0.8559 (tppt) REVERT: G 46 LYS cc_start: 0.9355 (tppt) cc_final: 0.9105 (tppt) REVERT: N 38 ARG cc_start: 0.8449 (ptt-90) cc_final: 0.8088 (ptt90) REVERT: N 46 GLU cc_start: 0.7414 (tt0) cc_final: 0.7002 (tt0) REVERT: N 51 ILE cc_start: 0.7494 (pt) cc_final: 0.7255 (pt) REVERT: N 53 GLN cc_start: 0.8817 (mp10) cc_final: 0.8379 (mp10) REVERT: N 60 TYR cc_start: 0.8585 (m-80) cc_final: 0.7428 (m-80) REVERT: N 80 TYR cc_start: 0.8086 (m-80) cc_final: 0.7753 (m-80) REVERT: N 87 LYS cc_start: 0.8407 (tppt) cc_final: 0.8125 (tppt) REVERT: R 170 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7351 (mptt) REVERT: R 227 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8312 (tm-30) REVERT: R 229 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6963 (tm-30) outliers start: 30 outliers final: 18 residues processed: 167 average time/residue: 0.1167 time to fit residues: 25.8362 Evaluate side-chains 151 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 3 GLN ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.103078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078654 restraints weight = 16567.081| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.97 r_work: 0.3133 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8461 Z= 0.118 Angle : 0.718 30.487 11504 Z= 0.317 Chirality : 0.067 1.930 1320 Planarity : 0.004 0.059 1446 Dihedral : 5.281 105.957 1173 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.85 % Allowed : 15.74 % Favored : 81.41 % 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: 0.51 (0.27), residues: 1027 helix: 1.71 (0.26), residues: 390 sheet: -0.51 (0.34), residues: 207 loop : -0.43 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.021 0.001 TYR R 299 PHE 0.014 0.001 PHE A 74 TRP 0.012 0.001 TRP B 297 HIS 0.003 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8458) covalent geometry : angle 0.71781 / 0.32 (11498) SS BOND : bond 0.00081 / 0.04 ( 3) SS BOND : angle 0.62745 / 0.29 ( 6) hydrogen bonds : bond 0.03209 / 2.16 ( 436) hydrogen bonds : angle 4.59074 / 3.27 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.5472 (tpt) cc_final: 0.4999 (mmm) REVERT: A 62 ILE cc_start: 0.8070 (tt) cc_final: 0.7594 (pt) REVERT: A 169 ARG cc_start: 0.8640 (ptp90) cc_final: 0.8419 (ptp90) REVERT: A 230 ASP cc_start: 0.8410 (m-30) cc_final: 0.8182 (m-30) REVERT: B 8 ARG cc_start: 0.9191 (mmt90) cc_final: 0.8967 (mmt90) REVERT: B 9 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8782 (pp30) REVERT: B 10 GLU cc_start: 0.8935 (tp30) cc_final: 0.8530 (tp30) REVERT: B 35 ASN cc_start: 0.8830 (m110) cc_final: 0.8449 (m-40) REVERT: B 280 LYS cc_start: 0.9053 (tttm) cc_final: 0.8305 (ttmm) REVERT: B 289 TYR cc_start: 0.8957 (m-80) cc_final: 0.8502 (m-80) REVERT: G 20 LYS cc_start: 0.9317 (mmtp) cc_final: 0.9082 (mmtp) REVERT: G 22 GLU cc_start: 0.9041 (tp30) cc_final: 0.8797 (tp30) REVERT: G 29 LYS cc_start: 0.8946 (tppt) cc_final: 0.8574 (tppt) REVERT: N 38 ARG cc_start: 0.8494 (ptt-90) cc_final: 0.8065 (ptt90) REVERT: N 46 GLU cc_start: 0.7564 (tt0) cc_final: 0.7112 (tt0) REVERT: N 53 GLN cc_start: 0.8830 (mp10) cc_final: 0.8537 (mp10) REVERT: N 60 TYR cc_start: 0.8534 (m-80) cc_final: 0.7448 (m-80) REVERT: N 68 PHE cc_start: 0.8538 (m-10) cc_final: 0.8259 (m-10) REVERT: N 72 ARG cc_start: 0.7631 (ptp-170) cc_final: 0.7365 (ptp-170) REVERT: N 80 TYR cc_start: 0.8178 (m-80) cc_final: 0.7861 (m-80) REVERT: N 82 GLN cc_start: 0.8395 (tp-100) cc_final: 0.8186 (tp-100) REVERT: N 87 LYS cc_start: 0.8504 (tppt) cc_final: 0.8260 (tppt) REVERT: R 170 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7390 (mptt) REVERT: R 238 MET cc_start: 0.8275 (tmm) cc_final: 0.8072 (tmm) outliers start: 25 outliers final: 20 residues processed: 165 average time/residue: 0.1128 time to fit residues: 24.7669 Evaluate side-chains 157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.104105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079573 restraints weight = 16741.763| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.99 r_work: 0.3155 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8461 Z= 0.113 Angle : 0.723 30.349 11504 Z= 0.317 Chirality : 0.066 1.928 1320 Planarity : 0.004 0.059 1446 Dihedral : 5.208 106.333 1173 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.85 % Allowed : 16.31 % Favored : 80.84 % 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: 0.61 (0.27), residues: 1027 helix: 1.85 (0.26), residues: 390 sheet: -0.48 (0.34), residues: 209 loop : -0.40 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 13 TYR 0.018 0.001 TYR R 308 PHE 0.013 0.001 PHE A 74 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 8458) covalent geometry : angle 0.72326 / 0.32 (11498) SS BOND : bond 0.00095 / 0.05 ( 3) SS BOND : angle 0.74532 / 0.44 ( 6) hydrogen bonds : bond 0.03141 / 2.12 ( 436) hydrogen bonds : angle 4.49745 / 3.22 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.5360 (tpt) cc_final: 0.4964 (mmm) REVERT: A 62 ILE cc_start: 0.8057 (tt) cc_final: 0.7594 (pt) REVERT: A 169 ARG cc_start: 0.8656 (ptp90) cc_final: 0.8425 (ptp90) REVERT: A 230 ASP cc_start: 0.8403 (m-30) cc_final: 0.8190 (m-30) REVERT: B 8 ARG cc_start: 0.9254 (mmt90) cc_final: 0.8989 (mmt90) REVERT: B 9 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8776 (pp30) REVERT: B 10 GLU cc_start: 0.8915 (tp30) cc_final: 0.8497 (tp30) REVERT: B 35 ASN cc_start: 0.8857 (m110) cc_final: 0.8453 (m-40) REVERT: B 280 LYS cc_start: 0.9003 (tttm) cc_final: 0.8312 (ttmm) REVERT: B 289 TYR cc_start: 0.8956 (m-80) cc_final: 0.8521 (m-80) REVERT: G 20 LYS cc_start: 0.9309 (mmtp) cc_final: 0.9085 (mmtp) REVERT: G 22 GLU cc_start: 0.9003 (tp30) cc_final: 0.8774 (tp30) REVERT: G 29 LYS cc_start: 0.8872 (tppt) cc_final: 0.8538 (tppt) REVERT: G 47 GLU cc_start: 0.8875 (mp0) cc_final: 0.8601 (mp0) REVERT: N 5 GLN cc_start: 0.7771 (mp10) cc_final: 0.7467 (mp10) REVERT: N 38 ARG cc_start: 0.8503 (ptt-90) cc_final: 0.8241 (ptt90) REVERT: N 46 GLU cc_start: 0.7614 (tt0) cc_final: 0.7264 (tt0) REVERT: N 53 GLN cc_start: 0.8800 (mp10) cc_final: 0.8391 (mp10) REVERT: N 60 TYR cc_start: 0.8577 (m-80) cc_final: 0.8149 (m-80) REVERT: N 80 TYR cc_start: 0.8211 (m-80) cc_final: 0.7957 (m-80) REVERT: N 87 LYS cc_start: 0.8482 (tppt) cc_final: 0.8248 (tppt) REVERT: R 170 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7332 (mptt) REVERT: R 173 PHE cc_start: 0.8252 (t80) cc_final: 0.7955 (t80) REVERT: R 227 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7806 (tt0) REVERT: R 307 ARG cc_start: 0.8733 (tmm160) cc_final: 0.8508 (ttp80) outliers start: 25 outliers final: 20 residues processed: 164 average time/residue: 0.1188 time to fit residues: 25.6208 Evaluate side-chains 155 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 0.0980 chunk 66 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.104093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079453 restraints weight = 16420.040| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.96 r_work: 0.3198 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8461 Z= 0.118 Angle : 0.728 30.296 11504 Z= 0.321 Chirality : 0.066 1.924 1320 Planarity : 0.004 0.058 1446 Dihedral : 5.225 106.902 1173 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.08 % Allowed : 16.88 % Favored : 80.05 % 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: 0.59 (0.27), residues: 1027 helix: 1.83 (0.26), residues: 390 sheet: -0.46 (0.33), residues: 227 loop : -0.43 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.020 0.001 TYR N 115 PHE 0.013 0.001 PHE A 74 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.000 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8458) covalent geometry : angle 0.72808 / 0.32 (11498) SS BOND : bond 0.00090 / 0.04 ( 3) SS BOND : angle 0.95407 / 0.55 ( 6) hydrogen bonds : bond 0.03216 / 2.16 ( 436) hydrogen bonds : angle 4.50064 / 3.22 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.5368 (tpt) cc_final: 0.4998 (mmm) REVERT: A 62 ILE cc_start: 0.8070 (tt) cc_final: 0.7598 (pt) REVERT: A 169 ARG cc_start: 0.8701 (ptp90) cc_final: 0.8410 (ptp90) REVERT: A 230 ASP cc_start: 0.8411 (m-30) cc_final: 0.8196 (m-30) REVERT: B 8 ARG cc_start: 0.9272 (mmt90) cc_final: 0.8965 (mmt90) REVERT: B 9 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8825 (pp30) REVERT: B 10 GLU cc_start: 0.8950 (tp30) cc_final: 0.8566 (tp30) REVERT: B 35 ASN cc_start: 0.8869 (m110) cc_final: 0.8464 (m-40) REVERT: B 280 LYS cc_start: 0.9010 (tttm) cc_final: 0.8307 (ttmm) REVERT: B 289 TYR cc_start: 0.8957 (m-80) cc_final: 0.8402 (m-80) REVERT: B 297 TRP cc_start: 0.8337 (m100) cc_final: 0.8091 (m100) REVERT: G 17 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9037 (mm-30) REVERT: G 22 GLU cc_start: 0.9052 (tp30) cc_final: 0.8808 (tp30) REVERT: G 29 LYS cc_start: 0.8840 (tppt) cc_final: 0.8487 (tppt) REVERT: G 47 GLU cc_start: 0.8867 (mp0) cc_final: 0.8587 (mp0) REVERT: N 46 GLU cc_start: 0.7699 (tt0) cc_final: 0.7360 (tt0) REVERT: N 60 TYR cc_start: 0.8577 (m-80) cc_final: 0.8132 (m-80) REVERT: N 80 TYR cc_start: 0.8207 (m-80) cc_final: 0.7924 (m-80) REVERT: N 87 LYS cc_start: 0.8500 (tppt) cc_final: 0.8219 (tppt) REVERT: R 170 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7328 (mptt) REVERT: R 173 PHE cc_start: 0.8162 (t80) cc_final: 0.7782 (t80) REVERT: R 227 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7728 (tt0) REVERT: R 307 ARG cc_start: 0.8748 (tmm160) cc_final: 0.8506 (ttp80) outliers start: 27 outliers final: 22 residues processed: 158 average time/residue: 0.1184 time to fit residues: 24.6540 Evaluate side-chains 157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 59 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.099652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074668 restraints weight = 16988.936| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.87 r_work: 0.3109 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8461 Z= 0.214 Angle : 0.786 30.495 11504 Z= 0.354 Chirality : 0.067 1.890 1320 Planarity : 0.004 0.059 1446 Dihedral : 5.553 106.814 1173 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.62 % Allowed : 17.22 % Favored : 80.16 % 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: 0.43 (0.27), residues: 1027 helix: 1.63 (0.26), residues: 391 sheet: -0.60 (0.33), residues: 223 loop : -0.40 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 72 TYR 0.025 0.002 TYR N 115 PHE 0.016 0.001 PHE A 74 TRP 0.012 0.002 TRP B 211 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 ( 8458) covalent geometry : angle 0.78597 / 0.35 (11498) SS BOND : bond 0.00223 / 0.11 ( 3) SS BOND : angle 1.06210 / 0.54 ( 6) hydrogen bonds : bond 0.03588 / 2.42 ( 436) hydrogen bonds : angle 4.76548 / 3.40 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.5417 (tpt) cc_final: 0.5158 (mmm) REVERT: A 62 ILE cc_start: 0.8095 (tt) cc_final: 0.7634 (pt) REVERT: A 169 ARG cc_start: 0.8706 (ptp90) cc_final: 0.8414 (ptp90) REVERT: B 8 ARG cc_start: 0.9256 (mmt90) cc_final: 0.8943 (mmt90) REVERT: B 9 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8830 (pp30) REVERT: B 10 GLU cc_start: 0.8993 (tp30) cc_final: 0.8567 (tp30) REVERT: B 35 ASN cc_start: 0.8868 (m110) cc_final: 0.8530 (m-40) REVERT: G 17 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8950 (mm-30) REVERT: G 22 GLU cc_start: 0.9002 (tp30) cc_final: 0.8710 (tp30) REVERT: G 29 LYS cc_start: 0.8908 (tppt) cc_final: 0.8571 (tppt) REVERT: N 5 GLN cc_start: 0.7849 (mp10) cc_final: 0.7541 (mp10) REVERT: N 19 ARG cc_start: 0.8417 (ttt90) cc_final: 0.8107 (ttt90) REVERT: N 38 ARG cc_start: 0.8660 (ptt-90) cc_final: 0.8195 (ptt90) REVERT: N 46 GLU cc_start: 0.7909 (tt0) cc_final: 0.7342 (tt0) REVERT: N 60 TYR cc_start: 0.8778 (m-80) cc_final: 0.8257 (m-80) REVERT: N 72 ARG cc_start: 0.7373 (ptp90) cc_final: 0.6970 (ptp-170) REVERT: N 78 THR cc_start: 0.9175 (m) cc_final: 0.8522 (p) REVERT: N 87 LYS cc_start: 0.8504 (tppt) cc_final: 0.8093 (tppt) REVERT: N 122 THR cc_start: 0.8323 (m) cc_final: 0.7875 (p) REVERT: R 170 LYS cc_start: 0.8455 (mmtt) cc_final: 0.7506 (mptt) REVERT: R 173 PHE cc_start: 0.8259 (t80) cc_final: 0.7995 (t80) outliers start: 23 outliers final: 19 residues processed: 166 average time/residue: 0.1137 time to fit residues: 25.1257 Evaluate side-chains 156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.101675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.076719 restraints weight = 16790.709| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.87 r_work: 0.3152 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8461 Z= 0.151 Angle : 0.783 30.079 11504 Z= 0.353 Chirality : 0.067 1.903 1320 Planarity : 0.004 0.059 1446 Dihedral : 5.487 107.063 1173 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.28 % Allowed : 18.59 % Favored : 79.13 % 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: 0.47 (0.27), residues: 1027 helix: 1.64 (0.26), residues: 392 sheet: -0.58 (0.33), residues: 222 loop : -0.36 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.022 0.001 TYR N 115 PHE 0.015 0.001 PHE A 74 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8458) covalent geometry : angle 0.78299 / 0.35 (11498) SS BOND : bond 0.00133 / 0.06 ( 3) SS BOND : angle 0.85119 / 0.46 ( 6) hydrogen bonds : bond 0.03437 / 2.31 ( 436) hydrogen bonds : angle 4.70207 / 3.36 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.5377 (tpt) cc_final: 0.5081 (mmm) REVERT: A 62 ILE cc_start: 0.8049 (tt) cc_final: 0.7568 (pt) REVERT: A 169 ARG cc_start: 0.8687 (ptp90) cc_final: 0.8404 (ptp90) REVERT: B 8 ARG cc_start: 0.9267 (mmt90) cc_final: 0.8939 (mmt90) REVERT: B 9 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8888 (pp30) REVERT: B 10 GLU cc_start: 0.8997 (tp30) cc_final: 0.8596 (tp30) REVERT: B 35 ASN cc_start: 0.8871 (m110) cc_final: 0.8462 (m110) REVERT: B 262 MET cc_start: 0.8016 (mmm) cc_final: 0.7785 (tpt) REVERT: B 280 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8457 (ttmm) REVERT: G 13 ARG cc_start: 0.9132 (ptp-110) cc_final: 0.8713 (mtm110) REVERT: G 14 LYS cc_start: 0.9485 (mmmt) cc_final: 0.9037 (tppt) REVERT: G 17 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8912 (mm-30) REVERT: G 22 GLU cc_start: 0.9011 (tp30) cc_final: 0.8736 (tp30) REVERT: G 29 LYS cc_start: 0.8827 (tppt) cc_final: 0.8510 (tppt) REVERT: G 47 GLU cc_start: 0.8897 (mp0) cc_final: 0.8682 (mp0) REVERT: N 5 GLN cc_start: 0.7820 (mp10) cc_final: 0.7470 (mp10) REVERT: N 19 ARG cc_start: 0.8528 (ttt90) cc_final: 0.8240 (ttt90) REVERT: N 38 ARG cc_start: 0.8703 (ptt-90) cc_final: 0.8136 (ptt90) REVERT: N 46 GLU cc_start: 0.7924 (tt0) cc_final: 0.7301 (tt0) REVERT: N 53 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7687 (mm110) REVERT: N 60 TYR cc_start: 0.8718 (m-80) cc_final: 0.8240 (m-80) REVERT: N 78 THR cc_start: 0.9091 (m) cc_final: 0.8480 (p) REVERT: N 87 LYS cc_start: 0.8481 (tppt) cc_final: 0.8136 (tppt) REVERT: R 170 LYS cc_start: 0.8418 (mmtt) cc_final: 0.7485 (mptt) REVERT: R 173 PHE cc_start: 0.8205 (t80) cc_final: 0.7903 (t80) outliers start: 20 outliers final: 20 residues processed: 162 average time/residue: 0.1158 time to fit residues: 24.8421 Evaluate side-chains 159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 6.9990 chunk 29 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 26 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.101772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.076840 restraints weight = 16895.897| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.89 r_work: 0.3154 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8461 Z= 0.186 Angle : 1.065 59.172 11504 Z= 0.578 Chirality : 0.069 1.904 1320 Planarity : 0.004 0.059 1446 Dihedral : 5.513 107.060 1173 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.51 % Allowed : 18.36 % Favored : 79.13 % Cbeta Deviations : 0.10 % 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: 0.47 (0.27), residues: 1027 helix: 1.65 (0.26), residues: 392 sheet: -0.59 (0.33), residues: 222 loop : -0.38 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.020 0.001 TYR N 115 PHE 0.015 0.001 PHE A 74 TRP 0.010 0.001 TRP B 169 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 8458) covalent geometry : angle 1.06555 / 0.58 (11498) SS BOND : bond 0.00160 / 0.07 ( 3) SS BOND : angle 0.86462 / 0.46 ( 6) hydrogen bonds : bond 0.03489 / 2.35 ( 436) hydrogen bonds : angle 4.70421 / 3.36 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2346.25 seconds wall clock time: 41 minutes 11.16 seconds (2471.16 seconds total)