Starting phenix.real_space_refine on Thu Mar 13 02:44:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjj_33229/03_2025/7xjj_33229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjj_33229/03_2025/7xjj_33229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xjj_33229/03_2025/7xjj_33229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjj_33229/03_2025/7xjj_33229.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjj_33229/03_2025/7xjj_33229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjj_33229/03_2025/7xjj_33229.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5559 2.51 5 N 1473 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8710 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1691 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 121 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "E" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2095 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 5.06, per 1000 atoms: 0.58 Number of scatterers: 8710 At special positions: 0 Unit cell: (88.047, 119.57, 125.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1621 8.00 N 1473 7.00 C 5559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 14 sheets defined 36.9% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.505A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.955A pdb=" N ILE A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'E' and resid 34 through 59 Processing helix chain 'E' and resid 69 through 98 Proline residue: E 90 - end of helix Processing helix chain 'E' and resid 103 through 139 removed outlier: 4.141A pdb=" N ILE E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 173 removed outlier: 3.613A pdb=" N ALA E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) Proline residue: E 169 - end of helix Processing helix chain 'E' and resid 193 through 231 removed outlier: 3.714A pdb=" N LYS E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Proline residue: E 212 - end of helix Processing helix chain 'E' and resid 235 through 272 Proline residue: E 262 - end of helix Processing helix chain 'E' and resid 278 through 304 Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.710A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.625A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.083A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 5.915A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.612A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.881A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.959A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.869A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.003A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.713A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.676A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 174 through 177 Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.689A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.247A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 143 through 148 447 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1405 1.27 - 1.41: 2326 1.41 - 1.55: 5090 1.55 - 1.69: 3 1.69 - 1.83: 80 Bond restraints: 8904 Sorted by residual: bond pdb=" C LEU A 23 " pdb=" O LEU A 23 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.17e-02 7.31e+03 8.14e+01 bond pdb=" CA LEU A 23 " pdb=" C LEU A 23 " ideal model delta sigma weight residual 1.523 1.409 0.114 1.30e-02 5.92e+03 7.68e+01 bond pdb=" C ASN A 22 " pdb=" O ASN A 22 " ideal model delta sigma weight residual 1.237 1.138 0.098 1.16e-02 7.43e+03 7.19e+01 bond pdb=" CA ASP A 26 " pdb=" C ASP A 26 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.29e-02 6.01e+03 4.89e+01 bond pdb=" C ASP A 26 " pdb=" O ASP A 26 " ideal model delta sigma weight residual 1.237 1.155 0.081 1.19e-02 7.06e+03 4.67e+01 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 11986 4.22 - 8.43: 93 8.43 - 12.65: 7 12.65 - 16.86: 2 16.86 - 21.08: 2 Bond angle restraints: 12090 Sorted by residual: angle pdb=" N LYS A 35 " pdb=" CA LYS A 35 " pdb=" C LYS A 35 " ideal model delta sigma weight residual 110.36 131.10 -20.74 1.55e+00 4.16e-01 1.79e+02 angle pdb=" N GLY E 157 " pdb=" CA GLY E 157 " pdb=" C GLY E 157 " ideal model delta sigma weight residual 112.83 101.71 11.12 1.22e+00 6.72e-01 8.31e+01 angle pdb=" CA PRO E 169 " pdb=" N PRO E 169 " pdb=" CD PRO E 169 " ideal model delta sigma weight residual 112.00 101.15 10.85 1.40e+00 5.10e-01 6.00e+01 angle pdb=" CA LYS A 32 " pdb=" C LYS A 32 " pdb=" N ASP A 33 " ideal model delta sigma weight residual 117.30 125.75 -8.45 1.16e+00 7.43e-01 5.31e+01 angle pdb=" CA CYS E 158 " pdb=" CB CYS E 158 " pdb=" SG CYS E 158 " ideal model delta sigma weight residual 114.40 98.13 16.27 2.30e+00 1.89e-01 5.01e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4708 18.00 - 36.00: 425 36.00 - 54.00: 72 54.00 - 72.00: 14 72.00 - 90.00: 4 Dihedral angle restraints: 5223 sinusoidal: 1965 harmonic: 3258 Sorted by residual: dihedral pdb=" C MET E 166 " pdb=" N MET E 166 " pdb=" CA MET E 166 " pdb=" CB MET E 166 " ideal model delta harmonic sigma weight residual -122.60 -149.39 26.79 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" N MET E 166 " pdb=" C MET E 166 " pdb=" CA MET E 166 " pdb=" CB MET E 166 " ideal model delta harmonic sigma weight residual 122.80 146.38 -23.58 0 2.50e+00 1.60e-01 8.90e+01 dihedral pdb=" C ILE A 28 " pdb=" N ILE A 28 " pdb=" CA ILE A 28 " pdb=" CB ILE A 28 " ideal model delta harmonic sigma weight residual -122.00 -137.24 15.24 0 2.50e+00 1.60e-01 3.72e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 1366 0.219 - 0.439: 8 0.439 - 0.658: 3 0.658 - 0.877: 2 0.877 - 1.097: 1 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CA MET E 166 " pdb=" N MET E 166 " pdb=" C MET E 166 " pdb=" CB MET E 166 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" CA PRO E 169 " pdb=" N PRO E 169 " pdb=" C PRO E 169 " pdb=" CB PRO E 169 " both_signs ideal model delta sigma weight residual False 2.72 1.95 0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CA LYS A 35 " pdb=" N LYS A 35 " pdb=" C LYS A 35 " pdb=" CB LYS A 35 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 1377 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 168 " -0.157 5.00e-02 4.00e+02 2.38e-01 9.05e+01 pdb=" N PRO E 169 " 0.411 5.00e-02 4.00e+02 pdb=" CA PRO E 169 " -0.135 5.00e-02 4.00e+02 pdb=" CD PRO E 169 " -0.119 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 156 " -0.025 2.00e-02 2.50e+03 5.16e-02 2.66e+01 pdb=" C VAL E 156 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL E 156 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY E 157 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 188 " 0.033 2.00e-02 2.50e+03 3.00e-02 2.24e+01 pdb=" CG TRP E 188 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E 188 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP E 188 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 188 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 188 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 188 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 188 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 188 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP E 188 " 0.001 2.00e-02 2.50e+03 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 47 2.40 - 3.02: 5273 3.02 - 3.65: 13354 3.65 - 4.27: 19467 4.27 - 4.90: 33595 Nonbonded interactions: 71736 Sorted by model distance: nonbonded pdb=" O LYS A 35 " pdb=" CG LEU A 36 " model vdw 1.771 3.470 nonbonded pdb=" O LYS A 35 " pdb=" CD2 LEU A 36 " model vdw 1.950 3.460 nonbonded pdb=" CE1 TYR E 113 " pdb=" CB ALA E 167 " model vdw 1.990 3.760 nonbonded pdb=" O ASN E 33 " pdb=" OG1 THR E 36 " model vdw 2.139 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.149 3.040 ... (remaining 71731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.050 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 : 0.007 0.114 8904 Z= 0.456 Angle : 0.879 21.081 12090 Z= 0.529 Chirality : 0.070 1.097 1380 Planarity : 0.008 0.238 1531 Dihedral : 14.108 89.998 3115 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.96 % Allowed : 1.49 % Favored : 97.55 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1104 helix: 2.09 (0.25), residues: 383 sheet: -0.58 (0.31), residues: 255 loop : -0.74 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP E 188 HIS 0.006 0.001 HIS E 289 PHE 0.018 0.001 PHE E 114 TYR 0.017 0.001 TYR S 101 ARG 0.008 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 28 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8114 (tp) REVERT: B 297 TRP cc_start: 0.7247 (m100) cc_final: 0.6894 (m100) REVERT: S 128 MET cc_start: 0.8094 (mmm) cc_final: 0.7627 (mmm) REVERT: S 217 CYS cc_start: 0.5906 (p) cc_final: 0.5491 (p) outliers start: 9 outliers final: 4 residues processed: 180 average time/residue: 0.2144 time to fit residues: 53.6044 Evaluate side-chains 146 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 169 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN E 76 ASN E 92 GLN E 196 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.199351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158717 restraints weight = 10880.902| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.93 r_work: 0.3733 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8904 Z= 0.173 Angle : 0.574 6.679 12090 Z= 0.301 Chirality : 0.042 0.164 1380 Planarity : 0.004 0.074 1531 Dihedral : 4.866 65.765 1216 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.06 % Allowed : 10.22 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1104 helix: 2.04 (0.25), residues: 385 sheet: -0.50 (0.30), residues: 281 loop : -0.99 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 188 HIS 0.006 0.001 HIS E 289 PHE 0.022 0.001 PHE E 177 TYR 0.016 0.001 TYR S 101 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7679 (mtm-85) REVERT: A 25 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 225 CYS cc_start: 0.8599 (m) cc_final: 0.8256 (p) REVERT: A 227 ASP cc_start: 0.7725 (t0) cc_final: 0.7433 (t0) REVERT: A 230 ASP cc_start: 0.8329 (m-30) cc_final: 0.8027 (m-30) REVERT: A 244 MET cc_start: 0.9103 (tpp) cc_final: 0.8665 (tpt) REVERT: B 253 PHE cc_start: 0.8054 (m-80) cc_final: 0.7728 (m-80) REVERT: E 195 ARG cc_start: 0.7276 (tmt170) cc_final: 0.6913 (ttp80) REVERT: E 200 TYR cc_start: 0.7850 (t80) cc_final: 0.7563 (t80) REVERT: S 65 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8066 (mtmt) REVERT: S 180 MET cc_start: 0.6791 (ptt) cc_final: 0.6021 (ptt) REVERT: S 217 CYS cc_start: 0.6338 (p) cc_final: 0.6025 (p) REVERT: S 219 GLN cc_start: 0.9201 (pp30) cc_final: 0.8907 (pp30) REVERT: S 221 LEU cc_start: 0.8667 (tp) cc_final: 0.8159 (tp) outliers start: 10 outliers final: 8 residues processed: 176 average time/residue: 0.2536 time to fit residues: 62.9968 Evaluate side-chains 157 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 159 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 307 GLN A 347 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.197163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.155748 restraints weight = 11079.319| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.97 r_work: 0.3688 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8904 Z= 0.186 Angle : 0.547 6.152 12090 Z= 0.288 Chirality : 0.042 0.161 1380 Planarity : 0.004 0.063 1531 Dihedral : 4.417 68.638 1207 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.92 % Allowed : 12.99 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1104 helix: 2.12 (0.25), residues: 390 sheet: -0.49 (0.30), residues: 281 loop : -0.98 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 188 HIS 0.004 0.001 HIS E 289 PHE 0.023 0.001 PHE E 177 TYR 0.014 0.001 TYR S 178 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.068 Fit side-chains REVERT: A 10 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7753 (mtm-85) REVERT: A 225 CYS cc_start: 0.8583 (m) cc_final: 0.8270 (p) REVERT: A 244 MET cc_start: 0.9101 (tpp) cc_final: 0.8662 (tpt) REVERT: B 298 ASP cc_start: 0.7604 (t70) cc_final: 0.7336 (t70) REVERT: B 301 LYS cc_start: 0.5627 (mmtt) cc_final: 0.5345 (mmtt) REVERT: E 158 CYS cc_start: 0.6987 (t) cc_final: 0.6768 (t) REVERT: E 195 ARG cc_start: 0.7090 (tmt170) cc_final: 0.6796 (ttp80) REVERT: E 197 LYS cc_start: 0.7357 (tppt) cc_final: 0.6623 (tptm) REVERT: G 38 MET cc_start: 0.6022 (OUTLIER) cc_final: 0.5627 (pmm) REVERT: S 34 MET cc_start: 0.8637 (mmm) cc_final: 0.8240 (mmm) REVERT: S 128 MET cc_start: 0.8501 (mmm) cc_final: 0.7104 (mmm) REVERT: S 180 MET cc_start: 0.6990 (ptt) cc_final: 0.6639 (ptt) REVERT: S 217 CYS cc_start: 0.6271 (p) cc_final: 0.5638 (p) REVERT: S 219 GLN cc_start: 0.9242 (pp30) cc_final: 0.8790 (pp30) REVERT: S 221 LEU cc_start: 0.8636 (tp) cc_final: 0.8053 (tp) outliers start: 18 outliers final: 11 residues processed: 169 average time/residue: 0.2442 time to fit residues: 57.7500 Evaluate side-chains 160 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 103 optimal weight: 0.0070 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS S 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.193656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.146084 restraints weight = 11136.486| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.15 r_work: 0.3621 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8904 Z= 0.272 Angle : 0.585 6.161 12090 Z= 0.307 Chirality : 0.043 0.182 1380 Planarity : 0.004 0.059 1531 Dihedral : 4.598 71.539 1205 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.24 % Allowed : 15.97 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1104 helix: 2.04 (0.25), residues: 391 sheet: -0.62 (0.31), residues: 273 loop : -0.92 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 188 HIS 0.005 0.001 HIS E 263 PHE 0.024 0.002 PHE E 177 TYR 0.023 0.002 TYR E 200 ARG 0.003 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.969 Fit side-chains REVERT: A 10 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7738 (mtm-85) REVERT: A 244 MET cc_start: 0.9110 (tpp) cc_final: 0.8670 (tpt) REVERT: B 217 MET cc_start: 0.7774 (ptp) cc_final: 0.7420 (ptm) REVERT: B 234 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6632 (m-10) REVERT: B 253 PHE cc_start: 0.8171 (m-80) cc_final: 0.7752 (m-80) REVERT: B 298 ASP cc_start: 0.7655 (t70) cc_final: 0.7372 (t70) REVERT: B 301 LYS cc_start: 0.5764 (mmtt) cc_final: 0.5482 (mmtt) REVERT: E 158 CYS cc_start: 0.7062 (t) cc_final: 0.6756 (t) REVERT: E 189 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7837 (mm-30) REVERT: E 195 ARG cc_start: 0.7098 (tmt170) cc_final: 0.6740 (ttp80) REVERT: E 196 HIS cc_start: 0.6986 (m90) cc_final: 0.6760 (m-70) REVERT: E 197 LYS cc_start: 0.7479 (tppt) cc_final: 0.6681 (tptm) REVERT: E 250 LEU cc_start: 0.8337 (tp) cc_final: 0.8121 (tp) REVERT: G 38 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5609 (pmm) REVERT: S 65 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8167 (mttp) REVERT: S 101 TYR cc_start: 0.7721 (m-10) cc_final: 0.7491 (m-10) REVERT: S 128 MET cc_start: 0.8381 (mmm) cc_final: 0.7161 (mmm) REVERT: S 180 MET cc_start: 0.7427 (ptt) cc_final: 0.6980 (ptt) REVERT: S 219 GLN cc_start: 0.9284 (pp30) cc_final: 0.8990 (pp30) REVERT: S 221 LEU cc_start: 0.8663 (tp) cc_final: 0.8098 (tp) REVERT: S 232 LYS cc_start: 0.8589 (tptp) cc_final: 0.8245 (tptt) outliers start: 21 outliers final: 12 residues processed: 174 average time/residue: 0.2666 time to fit residues: 67.0125 Evaluate side-chains 163 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 94 optimal weight: 0.0770 chunk 10 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.197433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.155266 restraints weight = 11059.641| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.99 r_work: 0.3675 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8904 Z= 0.171 Angle : 0.539 6.836 12090 Z= 0.281 Chirality : 0.041 0.172 1380 Planarity : 0.004 0.055 1531 Dihedral : 4.424 68.795 1205 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.13 % Allowed : 17.47 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1104 helix: 2.16 (0.25), residues: 391 sheet: -0.53 (0.31), residues: 268 loop : -0.79 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS E 289 PHE 0.021 0.001 PHE E 177 TYR 0.020 0.001 TYR E 200 ARG 0.002 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8468 (mp0) cc_final: 0.8199 (mp0) REVERT: A 225 CYS cc_start: 0.8565 (m) cc_final: 0.8356 (p) REVERT: A 244 MET cc_start: 0.9096 (tpp) cc_final: 0.8654 (tpt) REVERT: A 309 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: B 217 MET cc_start: 0.7815 (ptp) cc_final: 0.7503 (ptm) REVERT: B 234 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6676 (m-10) REVERT: B 253 PHE cc_start: 0.8059 (m-80) cc_final: 0.7722 (m-80) REVERT: B 298 ASP cc_start: 0.7633 (t70) cc_final: 0.7319 (t70) REVERT: B 301 LYS cc_start: 0.5622 (mmtt) cc_final: 0.5322 (mmtt) REVERT: E 158 CYS cc_start: 0.7080 (t) cc_final: 0.6798 (t) REVERT: E 195 ARG cc_start: 0.7257 (tmt170) cc_final: 0.6995 (ttp80) REVERT: E 197 LYS cc_start: 0.7444 (tppt) cc_final: 0.7172 (tptp) REVERT: E 200 TYR cc_start: 0.7241 (t80) cc_final: 0.7018 (t80) REVERT: E 250 LEU cc_start: 0.8365 (tp) cc_final: 0.8157 (tp) REVERT: G 38 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5527 (pmm) REVERT: S 34 MET cc_start: 0.8685 (mmm) cc_final: 0.8390 (mmm) REVERT: S 36 TRP cc_start: 0.7998 (m100) cc_final: 0.7507 (m100) REVERT: S 128 MET cc_start: 0.8097 (mmm) cc_final: 0.7812 (mtp) REVERT: S 180 MET cc_start: 0.7318 (ptt) cc_final: 0.6930 (ptt) REVERT: S 221 LEU cc_start: 0.8709 (tp) cc_final: 0.8207 (tp) REVERT: S 232 LYS cc_start: 0.8631 (tptp) cc_final: 0.8314 (tptt) outliers start: 20 outliers final: 14 residues processed: 173 average time/residue: 0.2026 time to fit residues: 48.6124 Evaluate side-chains 167 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 0.0980 chunk 99 optimal weight: 0.0270 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN E 92 GLN E 174 GLN E 190 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.195973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153513 restraints weight = 11004.443| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.98 r_work: 0.3662 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8904 Z= 0.217 Angle : 0.562 7.033 12090 Z= 0.292 Chirality : 0.042 0.181 1380 Planarity : 0.004 0.052 1531 Dihedral : 4.510 70.715 1205 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.77 % Allowed : 18.42 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1104 helix: 2.25 (0.25), residues: 385 sheet: -0.51 (0.31), residues: 275 loop : -0.82 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 188 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.001 PHE E 177 TYR 0.020 0.001 TYR E 200 ARG 0.006 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7582 (mtm-85) REVERT: A 244 MET cc_start: 0.9097 (tpp) cc_final: 0.8648 (tpt) REVERT: B 217 MET cc_start: 0.7753 (ptp) cc_final: 0.6948 (ptm) REVERT: B 219 ARG cc_start: 0.7979 (mmp80) cc_final: 0.7274 (mmp80) REVERT: B 220 GLN cc_start: 0.7185 (mt0) cc_final: 0.6864 (mt0) REVERT: B 234 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6710 (m-10) REVERT: B 253 PHE cc_start: 0.8092 (m-80) cc_final: 0.7725 (m-80) REVERT: B 298 ASP cc_start: 0.7648 (t70) cc_final: 0.7331 (t70) REVERT: B 301 LYS cc_start: 0.5756 (mmtt) cc_final: 0.5455 (mmtt) REVERT: E 158 CYS cc_start: 0.7110 (t) cc_final: 0.6838 (t) REVERT: E 195 ARG cc_start: 0.7199 (tmt170) cc_final: 0.6946 (ttp80) REVERT: E 197 LYS cc_start: 0.7333 (tppt) cc_final: 0.6715 (tptp) REVERT: E 200 TYR cc_start: 0.7259 (t80) cc_final: 0.6978 (t80) REVERT: E 250 LEU cc_start: 0.8395 (tp) cc_final: 0.8171 (tp) REVERT: G 38 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5506 (pmm) REVERT: S 34 MET cc_start: 0.8642 (mmm) cc_final: 0.8401 (mmm) REVERT: S 36 TRP cc_start: 0.8043 (m100) cc_final: 0.7584 (m100) REVERT: S 180 MET cc_start: 0.7443 (ptt) cc_final: 0.7166 (ptt) REVERT: S 221 LEU cc_start: 0.8600 (tp) cc_final: 0.8373 (tp) REVERT: S 232 LYS cc_start: 0.8695 (tptp) cc_final: 0.8448 (tptt) outliers start: 26 outliers final: 19 residues processed: 169 average time/residue: 0.2067 time to fit residues: 48.4815 Evaluate side-chains 181 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN B 88 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.193294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148958 restraints weight = 11217.487| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.89 r_work: 0.3618 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8904 Z= 0.284 Angle : 0.600 8.616 12090 Z= 0.311 Chirality : 0.043 0.184 1380 Planarity : 0.004 0.051 1531 Dihedral : 4.689 71.445 1205 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.30 % Allowed : 18.85 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1104 helix: 2.16 (0.25), residues: 385 sheet: -0.60 (0.30), residues: 280 loop : -0.89 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 188 HIS 0.005 0.001 HIS E 263 PHE 0.022 0.002 PHE E 177 TYR 0.019 0.002 TYR E 200 ARG 0.005 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7710 (mtm-85) REVERT: A 244 MET cc_start: 0.9103 (tpp) cc_final: 0.8655 (tpt) REVERT: A 309 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7419 (mt-10) REVERT: B 217 MET cc_start: 0.7745 (ptp) cc_final: 0.7006 (ptm) REVERT: B 219 ARG cc_start: 0.7964 (mmp80) cc_final: 0.7289 (mmp80) REVERT: B 220 GLN cc_start: 0.7112 (mt0) cc_final: 0.6784 (mt0) REVERT: B 234 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.6661 (m-10) REVERT: B 298 ASP cc_start: 0.7648 (t70) cc_final: 0.7315 (t70) REVERT: B 301 LYS cc_start: 0.5736 (mmtt) cc_final: 0.5414 (mmtt) REVERT: E 81 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7601 (t0) REVERT: E 158 CYS cc_start: 0.6931 (t) cc_final: 0.6636 (t) REVERT: E 187 CYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6692 (t) REVERT: E 197 LYS cc_start: 0.7286 (tppt) cc_final: 0.6639 (tptp) REVERT: E 250 LEU cc_start: 0.8304 (tp) cc_final: 0.8061 (tp) REVERT: G 38 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5556 (pmm) REVERT: S 34 MET cc_start: 0.8626 (mmm) cc_final: 0.8393 (mmm) REVERT: S 36 TRP cc_start: 0.8014 (m100) cc_final: 0.7544 (m100) REVERT: S 180 MET cc_start: 0.7447 (ptt) cc_final: 0.7167 (ptt) REVERT: S 219 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8972 (pp30) REVERT: S 232 LYS cc_start: 0.8695 (tptp) cc_final: 0.8466 (tptt) outliers start: 31 outliers final: 21 residues processed: 169 average time/residue: 0.1993 time to fit residues: 47.1998 Evaluate side-chains 170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 219 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.191830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.150456 restraints weight = 11568.274| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.55 r_work: 0.3623 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8904 Z= 0.367 Angle : 0.664 10.423 12090 Z= 0.346 Chirality : 0.045 0.193 1380 Planarity : 0.004 0.052 1531 Dihedral : 5.052 74.039 1205 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.51 % Allowed : 19.38 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1104 helix: 1.86 (0.25), residues: 385 sheet: -0.71 (0.31), residues: 268 loop : -1.07 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 188 HIS 0.007 0.001 HIS E 263 PHE 0.023 0.002 PHE E 177 TYR 0.020 0.002 TYR E 200 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.9106 (tpp) cc_final: 0.8633 (tpt) REVERT: A 309 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 199 PHE cc_start: 0.6700 (p90) cc_final: 0.6474 (p90) REVERT: B 217 MET cc_start: 0.7855 (ptp) cc_final: 0.7135 (ptm) REVERT: B 219 ARG cc_start: 0.8074 (mmp80) cc_final: 0.7376 (mmp80) REVERT: B 220 GLN cc_start: 0.7397 (mt0) cc_final: 0.6977 (mt0) REVERT: B 298 ASP cc_start: 0.7841 (t70) cc_final: 0.7594 (t70) REVERT: E 158 CYS cc_start: 0.6973 (t) cc_final: 0.6618 (t) REVERT: E 197 LYS cc_start: 0.7502 (tppt) cc_final: 0.6920 (tptp) REVERT: E 294 SER cc_start: 0.8899 (p) cc_final: 0.8661 (p) REVERT: G 38 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5745 (pmm) REVERT: S 36 TRP cc_start: 0.8160 (m100) cc_final: 0.7738 (m100) REVERT: S 162 LEU cc_start: 0.7977 (tp) cc_final: 0.7768 (tp) REVERT: S 180 MET cc_start: 0.7707 (ptt) cc_final: 0.7383 (ptt) REVERT: S 194 SER cc_start: 0.7613 (p) cc_final: 0.7369 (m) REVERT: S 232 LYS cc_start: 0.8797 (tptp) cc_final: 0.8563 (tptt) outliers start: 33 outliers final: 22 residues processed: 168 average time/residue: 0.1929 time to fit residues: 45.4689 Evaluate side-chains 170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.196223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.154620 restraints weight = 11142.867| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.95 r_work: 0.3669 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8904 Z= 0.197 Angle : 0.597 11.131 12090 Z= 0.312 Chirality : 0.043 0.235 1380 Planarity : 0.004 0.051 1531 Dihedral : 4.714 68.209 1205 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.56 % Allowed : 20.34 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1104 helix: 2.04 (0.26), residues: 385 sheet: -0.57 (0.32), residues: 260 loop : -0.88 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS E 289 PHE 0.025 0.001 PHE E 177 TYR 0.017 0.001 TYR S 178 ARG 0.004 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8435 (mp0) cc_final: 0.8142 (mp0) REVERT: A 10 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7783 (mtm-85) REVERT: A 28 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7374 (tp) REVERT: A 217 GLU cc_start: 0.8736 (tp30) cc_final: 0.8391 (tp30) REVERT: A 244 MET cc_start: 0.9046 (tpp) cc_final: 0.8577 (tpt) REVERT: A 309 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 217 MET cc_start: 0.7771 (ptp) cc_final: 0.7008 (ptm) REVERT: B 219 ARG cc_start: 0.7992 (mmp80) cc_final: 0.7320 (mmp80) REVERT: B 220 GLN cc_start: 0.7185 (mt0) cc_final: 0.6924 (mt0) REVERT: B 277 SER cc_start: 0.8811 (p) cc_final: 0.8566 (m) REVERT: E 158 CYS cc_start: 0.7076 (t) cc_final: 0.6799 (t) REVERT: E 197 LYS cc_start: 0.7264 (tppt) cc_final: 0.6701 (tptp) REVERT: E 250 LEU cc_start: 0.8267 (tp) cc_final: 0.8003 (tp) REVERT: E 293 TYR cc_start: 0.8079 (m-10) cc_final: 0.7794 (m-80) REVERT: G 38 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5519 (pmm) REVERT: S 36 TRP cc_start: 0.7982 (m100) cc_final: 0.7532 (m100) REVERT: S 180 MET cc_start: 0.7446 (ptt) cc_final: 0.7129 (ptt) REVERT: S 194 SER cc_start: 0.7446 (p) cc_final: 0.7204 (m) REVERT: S 232 LYS cc_start: 0.8760 (tptp) cc_final: 0.8528 (tptt) outliers start: 24 outliers final: 17 residues processed: 175 average time/residue: 0.2064 time to fit residues: 49.8534 Evaluate side-chains 168 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.0770 chunk 17 optimal weight: 0.0070 chunk 24 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN E 92 GLN E 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.200157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.159745 restraints weight = 11446.444| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.19 r_work: 0.3761 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8904 Z= 0.180 Angle : 0.587 8.757 12090 Z= 0.308 Chirality : 0.042 0.193 1380 Planarity : 0.004 0.050 1531 Dihedral : 4.612 69.386 1205 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.34 % Allowed : 20.66 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1104 helix: 2.11 (0.26), residues: 387 sheet: -0.57 (0.31), residues: 258 loop : -0.87 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS E 289 PHE 0.026 0.001 PHE E 177 TYR 0.016 0.001 TYR S 178 ARG 0.005 0.000 ARG A 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7817 (mtm-85) REVERT: A 28 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7452 (tp) REVERT: A 244 MET cc_start: 0.9049 (tpp) cc_final: 0.8563 (tpt) REVERT: A 309 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7872 (mt-10) REVERT: A 313 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7938 (ptt-90) REVERT: B 217 MET cc_start: 0.7817 (ptp) cc_final: 0.7282 (ptp) REVERT: B 219 ARG cc_start: 0.8013 (mmp80) cc_final: 0.7495 (mmp80) REVERT: B 220 GLN cc_start: 0.7277 (mt0) cc_final: 0.7063 (mt0) REVERT: B 253 PHE cc_start: 0.8085 (m-80) cc_final: 0.7763 (m-80) REVERT: E 86 LEU cc_start: 0.8245 (mt) cc_final: 0.8028 (mt) REVERT: E 158 CYS cc_start: 0.7056 (t) cc_final: 0.6775 (t) REVERT: E 174 GLN cc_start: 0.8054 (tp40) cc_final: 0.7482 (tp40) REVERT: E 188 TRP cc_start: 0.6898 (p90) cc_final: 0.6516 (p90) REVERT: E 197 LYS cc_start: 0.7482 (tppt) cc_final: 0.6890 (tptp) REVERT: G 38 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.5660 (pmm) REVERT: S 36 TRP cc_start: 0.8105 (m100) cc_final: 0.7805 (m100) REVERT: S 180 MET cc_start: 0.7639 (ptt) cc_final: 0.7381 (ptt) REVERT: S 200 PHE cc_start: 0.6344 (m-80) cc_final: 0.5780 (m-10) REVERT: S 232 LYS cc_start: 0.8788 (tptp) cc_final: 0.8528 (tptt) outliers start: 22 outliers final: 15 residues processed: 173 average time/residue: 0.2036 time to fit residues: 48.8599 Evaluate side-chains 170 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.200971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160773 restraints weight = 11483.463| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.25 r_work: 0.3779 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8904 Z= 0.181 Angle : 0.595 8.818 12090 Z= 0.309 Chirality : 0.042 0.206 1380 Planarity : 0.004 0.051 1531 Dihedral : 4.550 68.999 1205 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.13 % Allowed : 21.30 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1104 helix: 2.14 (0.26), residues: 387 sheet: -0.57 (0.31), residues: 262 loop : -0.81 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS E 289 PHE 0.025 0.001 PHE E 177 TYR 0.015 0.001 TYR B 289 ARG 0.004 0.000 ARG A 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4699.10 seconds wall clock time: 83 minutes 6.46 seconds (4986.46 seconds total)