Starting phenix.real_space_refine on Wed Mar 4 13:27:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0f_24789/03_2026/7s0f_24789_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0f_24789/03_2026/7s0f_24789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s0f_24789/03_2026/7s0f_24789_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0f_24789/03_2026/7s0f_24789_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s0f_24789/03_2026/7s0f_24789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0f_24789/03_2026/7s0f_24789.map" } resolution = 2.96 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= 1.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4461 2.51 5 N 1192 2.21 5 O 1293 1.98 5 H 6887 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13885 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4273 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5098 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3540 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 959 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.17 Number of scatterers: 13885 At special positions: 0 Unit cell: (85.88, 98.762, 132.041, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1293 8.00 N 1192 7.00 C 4461 6.00 H 6887 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 199 " distance=2.03 Simple disulfide: pdb=" SG CYS R 192 " - pdb=" SG CYS R 198 " 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: 1.15 Conformation dependent library (CDL) restraints added in 420.2 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 46.9% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 46 through 69 removed outlier: 3.985A pdb=" N LEU R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 105 removed outlier: 3.783A pdb=" N PHE R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 109 through 145 removed outlier: 4.087A pdb=" N LEU R 113 " --> pdb=" O TRP R 109 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS R 133 " --> pdb=" O ILE R 129 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'R' and resid 154 through 179 removed outlier: 4.144A pdb=" N LEU R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 189 through 195 Processing helix chain 'R' and resid 204 through 216 Processing helix chain 'R' and resid 216 through 239 Processing helix chain 'R' and resid 284 through 316 removed outlier: 3.523A pdb=" N LEU R 289 " --> pdb=" O GLU R 285 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 305 - end of helix removed outlier: 3.617A pdb=" N VAL R 309 " --> pdb=" O PRO R 305 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE R 311 " --> pdb=" O PHE R 307 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL R 314 " --> pdb=" O ASN R 310 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE R 315 " --> pdb=" O ILE R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 344 removed outlier: 3.646A pdb=" N VAL R 326 " --> pdb=" O ASP R 322 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER R 336 " --> pdb=" O GLY R 332 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA R 337 " --> pdb=" O TYR R 333 " (cutoff:3.500A) Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 346 through 356 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.921A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.664A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.530A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.564A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.450A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.841A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.997A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.533A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.516A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.538A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.586A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.870A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6859 1.03 - 1.23: 30 1.23 - 1.42: 3002 1.42 - 1.62: 4062 1.62 - 1.81: 72 Bond restraints: 14025 Sorted by residual: bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.437 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.417 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 1.457 1.491 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" CAE 5FW R 401 " pdb=" CAH 5FW R 401 " ideal model delta sigma weight residual 1.515 1.546 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" CAG 5FW R 401 " pdb=" CAJ 5FW R 401 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 14020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 24021 1.09 - 2.19: 1201 2.19 - 3.28: 25 3.28 - 4.38: 20 4.38 - 5.47: 1 Bond angle restraints: 25268 Sorted by residual: angle pdb=" CAJ 5FW R 401 " pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 114.52 109.05 5.47 3.00e+00 1.11e-01 3.33e+00 angle pdb=" C LEU R 175 " pdb=" CA LEU R 175 " pdb=" CB LEU R 175 " ideal model delta sigma weight residual 113.49 110.32 3.17 1.82e+00 3.02e-01 3.04e+00 angle pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 113.60 116.66 -3.06 1.90e+00 2.77e-01 2.60e+00 angle pdb=" C GLN B 9 " pdb=" N GLU B 10 " pdb=" CA GLU B 10 " ideal model delta sigma weight residual 120.28 118.02 2.26 1.44e+00 4.82e-01 2.47e+00 angle pdb=" C HIS A 188 " pdb=" N PHE A 189 " pdb=" CA PHE A 189 " ideal model delta sigma weight residual 121.85 119.23 2.62 1.77e+00 3.19e-01 2.19e+00 ... (remaining 25263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 5990 16.39 - 32.78: 438 32.78 - 49.17: 123 49.17 - 65.56: 36 65.56 - 81.95: 11 Dihedral angle restraints: 6598 sinusoidal: 3503 harmonic: 3095 Sorted by residual: dihedral pdb=" CA LYS B 127 " pdb=" C LYS B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA THR B 128 " pdb=" C THR B 128 " pdb=" N ARG B 129 " pdb=" CA ARG B 129 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP A 193 " pdb=" CB ASP A 193 " pdb=" CG ASP A 193 " pdb=" OD1 ASP A 193 " ideal model delta sinusoidal sigma weight residual -30.00 -84.11 54.11 1 2.00e+01 2.50e-03 9.93e+00 ... (remaining 6595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 975 0.058 - 0.115: 120 0.115 - 0.173: 13 0.173 - 0.231: 0 0.231 - 0.289: 1 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.58 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1106 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 218 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO R 219 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 219 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 219 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 95 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO R 96 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 96 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 96 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO A 282 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.014 5.00e-02 4.00e+02 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 925 2.22 - 2.81: 29471 2.81 - 3.41: 36220 3.41 - 4.00: 48683 4.00 - 4.60: 75421 Nonbonded interactions: 190720 Sorted by model distance: nonbonded pdb=" HG1 THR B 274 " pdb=" O VAL B 315 " model vdw 1.623 2.450 nonbonded pdb=" HE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 1.653 2.450 nonbonded pdb=" O LEU R 72 " pdb="HD22 ASN R 77 " model vdw 1.689 2.450 nonbonded pdb=" OE1 GLU A 298 " pdb=" H GLU A 298 " model vdw 1.713 2.450 nonbonded pdb=" O VAL R 160 " pdb=" HG1 THR R 164 " model vdw 1.723 2.450 ... (remaining 190715 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.390 Find NCS groups from input model: 0.040 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 0.084 7140 Z= 0.142 Angle : 0.449 5.474 9679 Z= 0.261 Chirality : 0.039 0.289 1109 Planarity : 0.002 0.030 1223 Dihedral : 13.976 81.945 2550 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 1.74 % Allowed : 13.50 % Favored : 84.76 % 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: -1.72 (0.25), residues: 880 helix: -0.02 (0.24), residues: 380 sheet: -1.28 (0.32), residues: 181 loop : -2.36 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 48 TYR 0.006 0.001 TYR B 105 PHE 0.009 0.001 PHE B 151 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7138) covalent geometry : angle 0.44927 ( 9675) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.56119 ( 4) hydrogen bonds : bond 0.13010 ( 379) hydrogen bonds : angle 5.10930 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 205 ARG cc_start: 0.6946 (ttm110) cc_final: 0.6077 (ttt-90) REVERT: R 233 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6728 (mm-30) REVERT: R 236 GLU cc_start: 0.7471 (tt0) cc_final: 0.7086 (tt0) REVERT: R 240 LYS cc_start: 0.6338 (mmtt) cc_final: 0.5972 (mmtp) REVERT: B 18 ILE cc_start: 0.7565 (mt) cc_final: 0.7319 (mt) REVERT: B 42 ARG cc_start: 0.7522 (mmm160) cc_final: 0.7281 (tpt-90) REVERT: B 172 GLU cc_start: 0.7788 (tt0) cc_final: 0.7569 (tt0) REVERT: B 226 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 258 ASP cc_start: 0.7932 (t0) cc_final: 0.7731 (t0) REVERT: B 331 SER cc_start: 0.9120 (t) cc_final: 0.8665 (t) REVERT: B 333 ASP cc_start: 0.7904 (p0) cc_final: 0.7688 (p0) REVERT: A 17 LYS cc_start: 0.7205 (mtpp) cc_final: 0.6967 (mtmm) REVERT: A 29 LYS cc_start: 0.8309 (tttt) cc_final: 0.7988 (tmtm) REVERT: A 205 ARG cc_start: 0.7033 (mtm110) cc_final: 0.6689 (tmm-80) REVERT: A 230 TYR cc_start: 0.8963 (p90) cc_final: 0.8572 (p90) REVERT: A 247 MET cc_start: 0.8194 (mtt) cc_final: 0.7970 (mmm) REVERT: A 248 LYS cc_start: 0.7490 (mttp) cc_final: 0.7043 (mttt) REVERT: A 251 ASP cc_start: 0.7494 (t0) cc_final: 0.7233 (t0) REVERT: A 257 LYS cc_start: 0.8743 (ptpp) cc_final: 0.8537 (ptmt) REVERT: A 330 LYS cc_start: 0.7173 (mttt) cc_final: 0.6791 (mtmm) REVERT: G 47 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7348 (mt-10) REVERT: G 58 GLU cc_start: 0.7553 (mp0) cc_final: 0.7352 (mp0) REVERT: G 64 LYS cc_start: 0.6833 (mmmt) cc_final: 0.6404 (mmmm) outliers start: 13 outliers final: 7 residues processed: 254 average time/residue: 0.9723 time to fit residues: 262.5594 Evaluate side-chains 193 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 238 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 329 ASN R 339 ASN B 36 ASN B 239 ASN A 52 GLN A 304 GLN A 347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.105511 restraints weight = 23339.390| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.28 r_work: 0.2974 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7140 Z= 0.157 Angle : 0.479 4.511 9679 Z= 0.265 Chirality : 0.039 0.138 1109 Planarity : 0.003 0.040 1223 Dihedral : 5.284 56.712 978 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.05 % Rotamer: Outliers : 3.07 % Allowed : 22.19 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.28), residues: 880 helix: 1.27 (0.26), residues: 382 sheet: -0.75 (0.35), residues: 176 loop : -1.85 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 62 TYR 0.008 0.001 TYR R 207 PHE 0.011 0.001 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7138) covalent geometry : angle 0.47913 ( 9675) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.55410 ( 4) hydrogen bonds : bond 0.04171 ( 379) hydrogen bonds : angle 4.20010 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.389 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: R 115 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: R 117 TRP cc_start: 0.8425 (t60) cc_final: 0.8142 (t60) REVERT: R 223 MET cc_start: 0.8736 (mtp) cc_final: 0.8480 (mtp) REVERT: R 233 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6868 (mm-30) REVERT: R 236 GLU cc_start: 0.7585 (tt0) cc_final: 0.7195 (tt0) REVERT: R 240 LYS cc_start: 0.6040 (mmtt) cc_final: 0.5820 (mmtp) REVERT: B 18 ILE cc_start: 0.7639 (mt) cc_final: 0.7359 (mt) REVERT: B 42 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7317 (tpt-90) REVERT: B 219 ARG cc_start: 0.8109 (mmt90) cc_final: 0.7659 (mtt-85) REVERT: B 226 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7972 (mt-10) REVERT: B 258 ASP cc_start: 0.8540 (t0) cc_final: 0.8282 (t0) REVERT: B 290 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: B 331 SER cc_start: 0.9358 (t) cc_final: 0.8915 (t) REVERT: B 333 ASP cc_start: 0.8223 (p0) cc_final: 0.7982 (p0) REVERT: A 17 LYS cc_start: 0.7493 (mtpp) cc_final: 0.7200 (mtmm) REVERT: A 29 LYS cc_start: 0.8338 (tttt) cc_final: 0.8089 (tptm) REVERT: A 230 TYR cc_start: 0.9108 (p90) cc_final: 0.8764 (p90) REVERT: A 247 MET cc_start: 0.8494 (mtt) cc_final: 0.8230 (mmm) REVERT: A 248 LYS cc_start: 0.7962 (mttp) cc_final: 0.7594 (mttt) REVERT: A 257 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8499 (ptmt) REVERT: A 273 LEU cc_start: 0.7332 (tp) cc_final: 0.7112 (tp) REVERT: A 330 LYS cc_start: 0.7262 (mttt) cc_final: 0.6839 (mtmm) REVERT: G 28 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8080 (pp) REVERT: G 47 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7895 (mt-10) REVERT: G 58 GLU cc_start: 0.7825 (mp0) cc_final: 0.7482 (mp0) REVERT: G 64 LYS cc_start: 0.6370 (mmmt) cc_final: 0.6086 (mmmt) outliers start: 23 outliers final: 10 residues processed: 214 average time/residue: 0.9785 time to fit residues: 222.7532 Evaluate side-chains 208 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 77 ASN R 339 ASN B 35 ASN B 239 ASN A 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106630 restraints weight = 23448.024| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.28 r_work: 0.2988 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7140 Z= 0.115 Angle : 0.442 4.042 9679 Z= 0.242 Chirality : 0.038 0.140 1109 Planarity : 0.003 0.043 1223 Dihedral : 4.378 42.925 972 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.88 % Allowed : 22.59 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.28 (0.29), residues: 880 helix: 2.01 (0.27), residues: 383 sheet: -0.50 (0.36), residues: 176 loop : -1.71 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 62 TYR 0.009 0.001 TYR R 207 PHE 0.008 0.001 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7138) covalent geometry : angle 0.44213 ( 9675) SS BOND : bond 0.00053 ( 2) SS BOND : angle 0.49467 ( 4) hydrogen bonds : bond 0.03641 ( 379) hydrogen bonds : angle 4.01398 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: R 117 TRP cc_start: 0.8393 (t60) cc_final: 0.8122 (t60) REVERT: R 233 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6882 (mm-30) REVERT: R 236 GLU cc_start: 0.7560 (tt0) cc_final: 0.7164 (tt0) REVERT: R 240 LYS cc_start: 0.5976 (mmtt) cc_final: 0.5754 (mmtp) REVERT: B 18 ILE cc_start: 0.7639 (mt) cc_final: 0.7422 (mt) REVERT: B 226 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 290 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: B 331 SER cc_start: 0.9328 (t) cc_final: 0.8839 (t) REVERT: B 333 ASP cc_start: 0.8164 (p0) cc_final: 0.7913 (p0) REVERT: A 17 LYS cc_start: 0.7476 (mtpp) cc_final: 0.7182 (mtmm) REVERT: A 205 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7128 (tmm-80) REVERT: A 230 TYR cc_start: 0.9112 (p90) cc_final: 0.8812 (p90) REVERT: A 247 MET cc_start: 0.8526 (mtt) cc_final: 0.8224 (mmm) REVERT: A 248 LYS cc_start: 0.7959 (mttp) cc_final: 0.7610 (mttt) REVERT: A 257 LYS cc_start: 0.8772 (ptpp) cc_final: 0.8477 (ptmt) REVERT: A 330 LYS cc_start: 0.7289 (mttt) cc_final: 0.6854 (mtmm) REVERT: G 28 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8140 (pp) REVERT: G 47 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7903 (mt-10) REVERT: G 58 GLU cc_start: 0.7808 (mp0) cc_final: 0.7471 (mp0) REVERT: G 64 LYS cc_start: 0.6243 (mmmt) cc_final: 0.5971 (mmmt) outliers start: 29 outliers final: 13 residues processed: 210 average time/residue: 0.8514 time to fit residues: 191.7552 Evaluate side-chains 202 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN B 35 ASN B 239 ASN A 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105839 restraints weight = 23526.499| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.23 r_work: 0.2962 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7140 Z= 0.168 Angle : 0.477 5.909 9679 Z= 0.263 Chirality : 0.039 0.140 1109 Planarity : 0.003 0.046 1223 Dihedral : 4.230 34.814 971 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 3.48 % Allowed : 24.20 % Favored : 72.33 % 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: 0.46 (0.29), residues: 880 helix: 2.18 (0.27), residues: 383 sheet: -0.42 (0.36), residues: 169 loop : -1.62 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 205 TYR 0.010 0.001 TYR R 207 PHE 0.012 0.001 PHE B 151 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7138) covalent geometry : angle 0.47644 ( 9675) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.80711 ( 4) hydrogen bonds : bond 0.03930 ( 379) hydrogen bonds : angle 4.06174 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.369 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: R 115 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: R 117 TRP cc_start: 0.8474 (t60) cc_final: 0.8204 (t60) REVERT: R 233 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6864 (mm-30) REVERT: R 236 GLU cc_start: 0.7603 (tt0) cc_final: 0.7184 (tt0) REVERT: R 240 LYS cc_start: 0.5974 (mmtt) cc_final: 0.5748 (mmtp) REVERT: B 18 ILE cc_start: 0.7709 (mt) cc_final: 0.7487 (mt) REVERT: B 226 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 331 SER cc_start: 0.9354 (t) cc_final: 0.8922 (t) REVERT: B 333 ASP cc_start: 0.8294 (p0) cc_final: 0.8049 (p0) REVERT: A 17 LYS cc_start: 0.7510 (mtpp) cc_final: 0.7221 (mtmm) REVERT: A 18 MET cc_start: 0.8172 (tpp) cc_final: 0.7830 (tpp) REVERT: A 209 LYS cc_start: 0.8711 (ttpp) cc_final: 0.8372 (ttpp) REVERT: A 247 MET cc_start: 0.8533 (mtt) cc_final: 0.8292 (mmm) REVERT: A 248 LYS cc_start: 0.8019 (mttp) cc_final: 0.7674 (mttt) REVERT: A 257 LYS cc_start: 0.8778 (ptpp) cc_final: 0.8410 (ptmt) REVERT: A 330 LYS cc_start: 0.7296 (mttt) cc_final: 0.6863 (mtmm) REVERT: G 28 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8140 (pp) REVERT: G 47 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7951 (mt-10) REVERT: G 58 GLU cc_start: 0.7858 (mp0) cc_final: 0.7448 (mp0) outliers start: 26 outliers final: 18 residues processed: 203 average time/residue: 0.8615 time to fit residues: 187.6048 Evaluate side-chains 201 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN A 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.104041 restraints weight = 23394.425| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.21 r_work: 0.2965 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7140 Z= 0.144 Angle : 0.469 4.969 9679 Z= 0.255 Chirality : 0.039 0.140 1109 Planarity : 0.003 0.045 1223 Dihedral : 4.211 34.706 971 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.16 % Rotamer: Outliers : 3.48 % Allowed : 24.47 % Favored : 72.06 % 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 (0.29), residues: 880 helix: 2.36 (0.27), residues: 383 sheet: -0.38 (0.37), residues: 169 loop : -1.60 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 205 TYR 0.009 0.001 TYR R 207 PHE 0.011 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7138) covalent geometry : angle 0.46873 ( 9675) SS BOND : bond 0.00049 ( 2) SS BOND : angle 0.55891 ( 4) hydrogen bonds : bond 0.03758 ( 379) hydrogen bonds : angle 4.03109 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.377 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: R 115 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: R 117 TRP cc_start: 0.8466 (t60) cc_final: 0.8233 (t60) REVERT: R 233 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6872 (mm-30) REVERT: R 236 GLU cc_start: 0.7579 (tt0) cc_final: 0.7166 (tt0) REVERT: R 240 LYS cc_start: 0.5986 (mmtt) cc_final: 0.5765 (mmtp) REVERT: B 18 ILE cc_start: 0.7716 (mt) cc_final: 0.7496 (mt) REVERT: B 226 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 258 ASP cc_start: 0.8256 (t0) cc_final: 0.7992 (t0) REVERT: B 331 SER cc_start: 0.9342 (t) cc_final: 0.8880 (t) REVERT: B 333 ASP cc_start: 0.8250 (p0) cc_final: 0.8009 (p0) REVERT: A 17 LYS cc_start: 0.7529 (mtpp) cc_final: 0.7239 (mtmm) REVERT: A 18 MET cc_start: 0.8156 (tpp) cc_final: 0.7813 (tpp) REVERT: A 247 MET cc_start: 0.8535 (mtt) cc_final: 0.8307 (mmm) REVERT: A 248 LYS cc_start: 0.8000 (mttp) cc_final: 0.7643 (mttt) REVERT: A 257 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8410 (ptmt) REVERT: A 330 LYS cc_start: 0.7299 (mttt) cc_final: 0.6857 (mtmm) REVERT: G 28 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8165 (pp) REVERT: G 47 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7947 (mt-10) REVERT: G 58 GLU cc_start: 0.7859 (mp0) cc_final: 0.7446 (mp0) outliers start: 26 outliers final: 17 residues processed: 199 average time/residue: 0.8753 time to fit residues: 186.5276 Evaluate side-chains 200 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.138643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.104545 restraints weight = 23474.788| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.21 r_work: 0.2969 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7140 Z= 0.128 Angle : 0.452 4.684 9679 Z= 0.246 Chirality : 0.039 0.140 1109 Planarity : 0.003 0.044 1223 Dihedral : 4.144 34.342 971 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.16 % Rotamer: Outliers : 2.81 % Allowed : 25.27 % Favored : 71.93 % 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: 0.78 (0.29), residues: 880 helix: 2.54 (0.27), residues: 383 sheet: -0.33 (0.37), residues: 169 loop : -1.55 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.008 0.001 TYR R 207 PHE 0.010 0.001 PHE B 292 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7138) covalent geometry : angle 0.45152 ( 9675) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.53679 ( 4) hydrogen bonds : bond 0.03581 ( 379) hydrogen bonds : angle 3.95109 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: R 117 TRP cc_start: 0.8455 (t60) cc_final: 0.8177 (t60) REVERT: R 233 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6844 (mm-30) REVERT: R 236 GLU cc_start: 0.7519 (tt0) cc_final: 0.7102 (tt0) REVERT: R 240 LYS cc_start: 0.5935 (mmtt) cc_final: 0.5711 (mmtp) REVERT: B 18 ILE cc_start: 0.7674 (mt) cc_final: 0.7462 (mt) REVERT: B 42 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7768 (mmt180) REVERT: B 226 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 331 SER cc_start: 0.9333 (t) cc_final: 0.8884 (t) REVERT: B 333 ASP cc_start: 0.8244 (p0) cc_final: 0.8018 (p0) REVERT: A 17 LYS cc_start: 0.7479 (mtpp) cc_final: 0.7176 (mtmm) REVERT: A 18 MET cc_start: 0.8150 (tpp) cc_final: 0.7796 (tpp) REVERT: A 33 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7080 (mm-30) REVERT: A 53 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7125 (mmt) REVERT: A 247 MET cc_start: 0.8547 (mtt) cc_final: 0.8310 (mmm) REVERT: A 248 LYS cc_start: 0.7985 (mttp) cc_final: 0.7684 (mttp) REVERT: A 253 ILE cc_start: 0.8843 (tt) cc_final: 0.8359 (mm) REVERT: A 257 LYS cc_start: 0.8806 (ptpp) cc_final: 0.8445 (ptmt) REVERT: A 314 LYS cc_start: 0.7044 (mmtt) cc_final: 0.6693 (mmmm) REVERT: A 330 LYS cc_start: 0.7257 (mttt) cc_final: 0.6806 (mtmm) REVERT: G 28 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8152 (pp) REVERT: G 47 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7965 (mt-10) REVERT: G 58 GLU cc_start: 0.7866 (mp0) cc_final: 0.7440 (mp0) outliers start: 21 outliers final: 14 residues processed: 193 average time/residue: 0.9292 time to fit residues: 191.9133 Evaluate side-chains 195 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.104069 restraints weight = 23262.387| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.27 r_work: 0.2960 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7140 Z= 0.134 Angle : 0.463 5.070 9679 Z= 0.252 Chirality : 0.039 0.140 1109 Planarity : 0.003 0.044 1223 Dihedral : 4.135 33.923 971 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 3.21 % Allowed : 24.87 % Favored : 71.93 % 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: 0.81 (0.29), residues: 880 helix: 2.53 (0.27), residues: 384 sheet: -0.28 (0.37), residues: 169 loop : -1.51 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.008 0.001 TYR R 207 PHE 0.010 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7138) covalent geometry : angle 0.46337 ( 9675) SS BOND : bond 0.00037 ( 2) SS BOND : angle 0.56060 ( 4) hydrogen bonds : bond 0.03607 ( 379) hydrogen bonds : angle 3.96457 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: R 117 TRP cc_start: 0.8455 (t60) cc_final: 0.8183 (t60) REVERT: R 233 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6818 (mm-30) REVERT: R 236 GLU cc_start: 0.7536 (tt0) cc_final: 0.7121 (tt0) REVERT: R 240 LYS cc_start: 0.6012 (mmtt) cc_final: 0.5800 (mmtp) REVERT: B 18 ILE cc_start: 0.7676 (mt) cc_final: 0.7472 (mt) REVERT: B 42 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7774 (mmt180) REVERT: B 226 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7972 (mt-10) REVERT: B 331 SER cc_start: 0.9309 (t) cc_final: 0.8877 (t) REVERT: B 333 ASP cc_start: 0.8233 (p0) cc_final: 0.8022 (p0) REVERT: A 17 LYS cc_start: 0.7438 (mtpp) cc_final: 0.7138 (mtmm) REVERT: A 18 MET cc_start: 0.8128 (tpp) cc_final: 0.7765 (tpp) REVERT: A 53 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7065 (mmt) REVERT: A 247 MET cc_start: 0.8454 (mtt) cc_final: 0.8248 (mmm) REVERT: A 248 LYS cc_start: 0.7953 (mttp) cc_final: 0.7658 (mttp) REVERT: A 253 ILE cc_start: 0.8815 (tt) cc_final: 0.8376 (mm) REVERT: A 257 LYS cc_start: 0.8791 (ptpp) cc_final: 0.8414 (ptmt) REVERT: A 314 LYS cc_start: 0.7103 (mmtt) cc_final: 0.6757 (mmmm) REVERT: A 330 LYS cc_start: 0.7225 (mttt) cc_final: 0.6786 (mtmm) REVERT: G 28 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8081 (pp) REVERT: G 47 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7960 (mt-10) REVERT: G 58 GLU cc_start: 0.7855 (mp0) cc_final: 0.7418 (mp0) outliers start: 24 outliers final: 19 residues processed: 193 average time/residue: 0.9042 time to fit residues: 186.9340 Evaluate side-chains 202 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN A 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.103287 restraints weight = 23315.694| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.16 r_work: 0.2956 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7140 Z= 0.163 Angle : 0.477 5.251 9679 Z= 0.262 Chirality : 0.039 0.140 1109 Planarity : 0.003 0.044 1223 Dihedral : 4.199 33.286 971 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 3.88 % Allowed : 24.20 % Favored : 71.93 % 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: 0.77 (0.29), residues: 880 helix: 2.49 (0.27), residues: 384 sheet: -0.29 (0.37), residues: 169 loop : -1.53 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.008 0.001 TYR R 207 PHE 0.012 0.001 PHE B 151 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7138) covalent geometry : angle 0.47710 ( 9675) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.60854 ( 4) hydrogen bonds : bond 0.03823 ( 379) hydrogen bonds : angle 4.01616 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: R 233 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6828 (mm-30) REVERT: R 236 GLU cc_start: 0.7554 (tt0) cc_final: 0.7121 (tt0) REVERT: R 240 LYS cc_start: 0.6047 (mmtt) cc_final: 0.5839 (mmtp) REVERT: B 42 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7750 (mmt180) REVERT: B 226 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7969 (mt-10) REVERT: B 331 SER cc_start: 0.9328 (t) cc_final: 0.8896 (t) REVERT: B 333 ASP cc_start: 0.8256 (p0) cc_final: 0.8036 (p0) REVERT: A 17 LYS cc_start: 0.7473 (mtpp) cc_final: 0.7172 (mtmm) REVERT: A 18 MET cc_start: 0.8114 (tpp) cc_final: 0.7745 (tpp) REVERT: A 33 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 248 LYS cc_start: 0.7934 (mttp) cc_final: 0.7645 (mttp) REVERT: A 257 LYS cc_start: 0.8784 (ptpp) cc_final: 0.8424 (ptmt) REVERT: A 314 LYS cc_start: 0.7118 (mmtt) cc_final: 0.6773 (mmmm) REVERT: A 330 LYS cc_start: 0.7223 (mttt) cc_final: 0.6805 (mtmm) REVERT: G 28 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8100 (pp) REVERT: G 47 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8023 (mt-10) REVERT: G 58 GLU cc_start: 0.7830 (mp0) cc_final: 0.7383 (mp0) outliers start: 29 outliers final: 20 residues processed: 201 average time/residue: 0.8670 time to fit residues: 186.6322 Evaluate side-chains 207 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.102126 restraints weight = 23424.516| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.24 r_work: 0.2936 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7140 Z= 0.184 Angle : 0.491 5.288 9679 Z= 0.270 Chirality : 0.039 0.140 1109 Planarity : 0.003 0.045 1223 Dihedral : 4.279 32.898 971 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 3.07 % Allowed : 25.67 % Favored : 71.26 % 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: 0.66 (0.29), residues: 880 helix: 2.38 (0.27), residues: 384 sheet: -0.27 (0.37), residues: 170 loop : -1.61 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.008 0.001 TYR R 207 PHE 0.013 0.001 PHE B 151 TRP 0.010 0.001 TRP R 117 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7138) covalent geometry : angle 0.49059 ( 9675) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.67209 ( 4) hydrogen bonds : bond 0.03982 ( 379) hydrogen bonds : angle 4.09698 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: R 233 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6889 (mm-30) REVERT: B 42 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7777 (mmt180) REVERT: B 226 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7969 (mt-10) REVERT: B 331 SER cc_start: 0.9336 (t) cc_final: 0.8935 (t) REVERT: B 333 ASP cc_start: 0.8291 (p0) cc_final: 0.8077 (p0) REVERT: A 17 LYS cc_start: 0.7504 (mtpp) cc_final: 0.7205 (mtmm) REVERT: A 18 MET cc_start: 0.8139 (tpp) cc_final: 0.7771 (tpp) REVERT: A 33 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7226 (mm-30) REVERT: A 248 LYS cc_start: 0.8045 (mttp) cc_final: 0.7748 (mttp) REVERT: A 257 LYS cc_start: 0.8785 (ptpp) cc_final: 0.8420 (ptmt) REVERT: A 314 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6782 (mmmm) REVERT: A 330 LYS cc_start: 0.7278 (mttt) cc_final: 0.6871 (mtmm) REVERT: G 47 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7978 (mt-10) REVERT: G 58 GLU cc_start: 0.7838 (mp0) cc_final: 0.7383 (mp0) outliers start: 23 outliers final: 19 residues processed: 202 average time/residue: 0.8777 time to fit residues: 190.2051 Evaluate side-chains 207 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.104516 restraints weight = 23363.273| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.26 r_work: 0.2970 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7140 Z= 0.105 Angle : 0.463 5.688 9679 Z= 0.249 Chirality : 0.038 0.141 1109 Planarity : 0.004 0.077 1223 Dihedral : 4.127 33.490 971 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.27 % Favored : 97.61 % Rotamer: Outliers : 2.27 % Allowed : 27.54 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.93 (0.29), residues: 880 helix: 2.59 (0.27), residues: 384 sheet: -0.11 (0.38), residues: 174 loop : -1.48 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 205 TYR 0.007 0.001 TYR R 207 PHE 0.009 0.001 PHE A 189 TRP 0.013 0.001 TRP R 117 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7138) covalent geometry : angle 0.46335 ( 9675) SS BOND : bond 0.00041 ( 2) SS BOND : angle 0.54970 ( 4) hydrogen bonds : bond 0.03403 ( 379) hydrogen bonds : angle 3.96158 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: R 169 SER cc_start: 0.9172 (t) cc_final: 0.8943 (p) REVERT: R 205 ARG cc_start: 0.7746 (tpp-160) cc_final: 0.6005 (tmt-80) REVERT: R 213 ILE cc_start: 0.8659 (mt) cc_final: 0.8434 (mm) REVERT: R 233 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6835 (mm-30) REVERT: R 236 GLU cc_start: 0.7465 (tt0) cc_final: 0.7093 (tt0) REVERT: B 226 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7982 (mt-10) REVERT: B 333 ASP cc_start: 0.8215 (p0) cc_final: 0.7911 (p0) REVERT: B 334 SER cc_start: 0.8798 (m) cc_final: 0.8439 (p) REVERT: A 17 LYS cc_start: 0.7457 (mtpp) cc_final: 0.7150 (mtmm) REVERT: A 18 MET cc_start: 0.8139 (tpp) cc_final: 0.7772 (tpp) REVERT: A 33 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7192 (mm-30) REVERT: A 53 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7127 (mmt) REVERT: A 248 LYS cc_start: 0.8021 (mttp) cc_final: 0.7728 (mttp) REVERT: A 257 LYS cc_start: 0.8794 (ptpp) cc_final: 0.8429 (ptmt) REVERT: A 314 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6766 (mmmm) REVERT: A 330 LYS cc_start: 0.7247 (mttt) cc_final: 0.6825 (mtmm) REVERT: G 47 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7957 (mt-10) REVERT: G 58 GLU cc_start: 0.7852 (mp0) cc_final: 0.7423 (mp0) outliers start: 17 outliers final: 12 residues processed: 205 average time/residue: 0.8441 time to fit residues: 186.1808 Evaluate side-chains 202 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.0040 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 0.0670 chunk 53 optimal weight: 0.3980 overall best weight: 0.2328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.106222 restraints weight = 23328.404| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.28 r_work: 0.3000 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7140 Z= 0.090 Angle : 0.451 5.078 9679 Z= 0.240 Chirality : 0.038 0.141 1109 Planarity : 0.004 0.070 1223 Dihedral : 3.948 32.932 971 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.34 % Allowed : 28.74 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.06 (0.29), residues: 880 helix: 2.73 (0.27), residues: 384 sheet: -0.11 (0.38), residues: 169 loop : -1.40 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 205 TYR 0.006 0.001 TYR R 207 PHE 0.008 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 7138) covalent geometry : angle 0.45087 ( 9675) SS BOND : bond 0.00038 ( 2) SS BOND : angle 0.49590 ( 4) hydrogen bonds : bond 0.03095 ( 379) hydrogen bonds : angle 3.86841 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5679.92 seconds wall clock time: 96 minutes 29.32 seconds (5789.32 seconds total)