Starting phenix.real_space_refine on Fri Aug 22 21:13:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbj_39903/08_2025/8zbj_39903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbj_39903/08_2025/8zbj_39903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zbj_39903/08_2025/8zbj_39903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbj_39903/08_2025/8zbj_39903.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbj_39903/08_2025/8zbj_39903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbj_39903/08_2025/8zbj_39903.cif" } resolution = 2.94 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= 0.001 sd= 0.032 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 58 5.16 5 C 5168 2.51 5 N 1387 2.21 5 O 1472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8085 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 78 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "C" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "E" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 419 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "F" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1689 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain breaks: 2 Chain: "R" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2034 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 249} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1281 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 166} Chain breaks: 5 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 2.21, per 1000 atoms: 0.27 Number of scatterers: 8085 At special positions: 0 Unit cell: (106.848, 106.848, 122.112, 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 58 16.00 O 1472 8.00 N 1387 7.00 C 5168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 197 " - pdb=" SG CYS F 267 " distance=2.04 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 444.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 36.6% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 6 through 26 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.647A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 24 removed outlier: 4.058A pdb=" N LYS E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.790A pdb=" N THR F 129 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 67 removed outlier: 3.907A pdb=" N VAL R 45 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU R 48 " --> pdb=" O PRO R 44 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG R 67 " --> pdb=" O TYR R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 92 removed outlier: 3.694A pdb=" N ASN R 81 " --> pdb=" O ILE R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 103 removed outlier: 3.709A pdb=" N ALA R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 143 removed outlier: 3.841A pdb=" N LEU R 114 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR R 117 " --> pdb=" O ARG R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 170 removed outlier: 3.650A pdb=" N MET R 170 " --> pdb=" O LEU R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 178 Processing helix chain 'R' and resid 193 through 207 removed outlier: 3.795A pdb=" N TRP R 197 " --> pdb=" O PRO R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 229 removed outlier: 3.726A pdb=" N ILE R 224 " --> pdb=" O CYS R 220 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL R 225 " --> pdb=" O TYR R 221 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 274 removed outlier: 3.698A pdb=" N LYS R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG R 248 " --> pdb=" O ARG R 244 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Proline residue: R 263 - end of helix removed outlier: 3.735A pdb=" N VAL R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 306 removed outlier: 3.889A pdb=" N ASN R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 316 removed outlier: 3.546A pdb=" N GLN R 313 " --> pdb=" O ASP R 309 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN R 316 " --> pdb=" O ARG R 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.541A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.892A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 removed outlier: 4.160A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.637A pdb=" N GLY C 330 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.930A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.762A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.813A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.636A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.443A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.433A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 285 " --> pdb=" O TRP C 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 41 through 46 removed outlier: 3.630A pdb=" N SER F 59 " --> pdb=" O SER F 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.198A pdb=" N GLY F 48 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET F 72 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR F 88 " --> pdb=" O MET F 72 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP F 74 " --> pdb=" O VAL F 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 178 through 179 Processing sheet with id=AB2, first strand: chain 'F' and resid 232 through 233 removed outlier: 6.720A pdb=" N TRP F 214 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR F 228 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU F 212 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.525A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1640 1.33 - 1.45: 2021 1.45 - 1.57: 4508 1.57 - 1.69: 1 1.69 - 1.82: 83 Bond restraints: 8253 Sorted by residual: bond pdb=" N LYS S 9 " pdb=" CA LYS S 9 " ideal model delta sigma weight residual 1.457 1.405 0.052 1.29e-02 6.01e+03 1.64e+01 bond pdb=" C TRP S 8 " pdb=" O TRP S 8 " ideal model delta sigma weight residual 1.234 1.207 0.027 1.20e-02 6.94e+03 5.18e+00 bond pdb=" CB PRO C 194 " pdb=" CG PRO C 194 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.44e+00 bond pdb=" C LEU R 172 " pdb=" N PRO R 173 " ideal model delta sigma weight residual 1.335 1.364 -0.028 1.36e-02 5.41e+03 4.31e+00 bond pdb=" C TRP S 8 " pdb=" N LYS S 9 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.08e+00 ... (remaining 8248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 11058 2.50 - 5.00: 100 5.00 - 7.50: 30 7.50 - 10.00: 7 10.00 - 12.50: 1 Bond angle restraints: 11196 Sorted by residual: angle pdb=" CA PRO C 194 " pdb=" N PRO C 194 " pdb=" CD PRO C 194 " ideal model delta sigma weight residual 112.00 103.65 8.35 1.40e+00 5.10e-01 3.56e+01 angle pdb=" C PHE S 7 " pdb=" N TRP S 8 " pdb=" CA TRP S 8 " ideal model delta sigma weight residual 120.82 127.36 -6.54 1.41e+00 5.03e-01 2.15e+01 angle pdb=" N PRO C 194 " pdb=" CD PRO C 194 " pdb=" CG PRO C 194 " ideal model delta sigma weight residual 103.20 96.60 6.60 1.50e+00 4.44e-01 1.93e+01 angle pdb=" N TRP S 8 " pdb=" CA TRP S 8 " pdb=" C TRP S 8 " ideal model delta sigma weight residual 110.10 116.28 -6.18 1.49e+00 4.50e-01 1.72e+01 angle pdb=" CA LEU R 172 " pdb=" CB LEU R 172 " pdb=" CG LEU R 172 " ideal model delta sigma weight residual 116.30 128.80 -12.50 3.50e+00 8.16e-02 1.28e+01 ... (remaining 11191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4139 17.05 - 34.09: 518 34.09 - 51.14: 150 51.14 - 68.19: 27 68.19 - 85.24: 12 Dihedral angle restraints: 4846 sinusoidal: 1827 harmonic: 3019 Sorted by residual: dihedral pdb=" CA LEU R 93 " pdb=" C LEU R 93 " pdb=" N PRO R 94 " pdb=" CA PRO R 94 " ideal model delta harmonic sigma weight residual -180.00 -158.99 -21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TYR F 139 " pdb=" C TYR F 139 " pdb=" N TYR F 140 " pdb=" CA TYR F 140 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA TYR F 273 " pdb=" C TYR F 273 " pdb=" N PRO F 274 " pdb=" CA PRO F 274 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 913 0.040 - 0.080: 268 0.080 - 0.119: 92 0.119 - 0.159: 14 0.159 - 0.199: 2 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CA TRP S 8 " pdb=" N TRP S 8 " pdb=" C TRP S 8 " pdb=" CB TRP S 8 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA TYR F 273 " pdb=" N TYR F 273 " pdb=" C TYR F 273 " pdb=" CB TYR F 273 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA TYR C 59 " pdb=" N TYR C 59 " pdb=" C TYR C 59 " pdb=" CB TYR C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 1286 not shown) Planarity restraints: 1409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " -0.076 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO C 194 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 105 " -0.024 2.00e-02 2.50e+03 2.23e-02 1.24e+01 pdb=" CG TRP R 105 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP R 105 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP R 105 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 105 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 105 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 105 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 105 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP R 105 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 48 " -0.051 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO E 49 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 49 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 49 " -0.043 5.00e-02 4.00e+02 ... (remaining 1406 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1611 2.78 - 3.31: 7296 3.31 - 3.84: 12882 3.84 - 4.37: 14762 4.37 - 4.90: 26503 Nonbonded interactions: 63054 Sorted by model distance: nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP R 86 " pdb=" OG SER R 297 " model vdw 2.257 3.040 nonbonded pdb=" O ALA E 56 " pdb=" NH2 ARG E 62 " model vdw 2.262 3.120 nonbonded pdb=" O ALA C 257 " pdb=" NE2 GLN C 259 " model vdw 2.275 3.120 nonbonded pdb=" O SER R 146 " pdb=" NH1 ARG R 149 " model vdw 2.293 3.120 ... (remaining 63049 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.380 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 0.105 8255 Z= 0.164 Angle : 0.729 12.505 11200 Z= 0.373 Chirality : 0.043 0.199 1289 Planarity : 0.005 0.109 1409 Dihedral : 16.704 85.236 2888 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.46 % Rotamer: Outliers : 3.36 % Allowed : 31.37 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.26), residues: 1017 helix: 1.90 (0.29), residues: 345 sheet: 0.16 (0.33), residues: 251 loop : -1.25 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 313 TYR 0.018 0.001 TYR R 294 PHE 0.028 0.002 PHE R 306 TRP 0.061 0.002 TRP R 105 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8253) covalent geometry : angle 0.72946 (11196) SS BOND : bond 0.00458 ( 2) SS BOND : angle 0.77882 ( 4) hydrogen bonds : bond 0.16948 ( 379) hydrogen bonds : angle 5.62431 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 212 ASP cc_start: 0.7104 (t70) cc_final: 0.6374 (t0) REVERT: C 215 GLU cc_start: 0.7822 (mp0) cc_final: 0.7168 (mp0) REVERT: C 325 MET cc_start: 0.8528 (tpp) cc_final: 0.8223 (tpp) outliers start: 29 outliers final: 24 residues processed: 135 average time/residue: 0.5006 time to fit residues: 72.5858 Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 340 ASN E 59 ASN F 115 ASN R 58 ASN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.202327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131621 restraints weight = 9324.771| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.77 r_work: 0.3416 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 8255 Z= 0.303 Angle : 0.783 12.975 11200 Z= 0.393 Chirality : 0.048 0.276 1289 Planarity : 0.006 0.069 1409 Dihedral : 7.559 58.855 1162 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 8.10 % Allowed : 26.16 % Favored : 65.74 % 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 aren not related in a simple way. whole: 0.02 (0.26), residues: 1017 helix: 1.60 (0.28), residues: 349 sheet: -0.12 (0.32), residues: 261 loop : -1.28 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 313 TYR 0.022 0.003 TYR R 294 PHE 0.038 0.002 PHE C 199 TRP 0.027 0.002 TRP R 105 HIS 0.008 0.002 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00734 ( 8253) covalent geometry : angle 0.78243 (11196) SS BOND : bond 0.00678 ( 2) SS BOND : angle 1.60256 ( 4) hydrogen bonds : bond 0.05578 ( 379) hydrogen bonds : angle 4.80844 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 118 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: C 212 ASP cc_start: 0.7696 (t70) cc_final: 0.7148 (t0) REVERT: C 215 GLU cc_start: 0.7963 (mp0) cc_final: 0.7400 (mp0) REVERT: C 255 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8090 (mp) REVERT: C 325 MET cc_start: 0.8686 (tpp) cc_final: 0.8327 (tpp) REVERT: F 115 ASN cc_start: 0.7927 (m-40) cc_final: 0.7690 (m-40) REVERT: F 198 ARG cc_start: 0.7267 (ttm110) cc_final: 0.6408 (mtm180) REVERT: F 261 ASP cc_start: 0.7426 (m-30) cc_final: 0.6491 (t0) REVERT: A 198 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7216 (tmm) REVERT: A 308 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7340 (mp0) outliers start: 70 outliers final: 39 residues processed: 165 average time/residue: 0.4381 time to fit residues: 78.3758 Evaluate side-chains 155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 63 optimal weight: 0.0020 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN R 58 ASN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.207218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139579 restraints weight = 9066.338| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.54 r_work: 0.3506 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8255 Z= 0.114 Angle : 0.609 11.456 11200 Z= 0.297 Chirality : 0.042 0.173 1289 Planarity : 0.004 0.053 1409 Dihedral : 6.161 59.672 1142 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 7.41 % Allowed : 27.55 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.26), residues: 1017 helix: 1.80 (0.28), residues: 353 sheet: -0.01 (0.32), residues: 250 loop : -1.31 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 198 TYR 0.015 0.001 TYR F 228 PHE 0.016 0.001 PHE C 199 TRP 0.029 0.001 TRP R 105 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8253) covalent geometry : angle 0.60841 (11196) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.99257 ( 4) hydrogen bonds : bond 0.04021 ( 379) hydrogen bonds : angle 4.40989 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 108 time to evaluate : 0.322 Fit side-chains REVERT: C 153 ASP cc_start: 0.7500 (m-30) cc_final: 0.7272 (m-30) REVERT: C 212 ASP cc_start: 0.7507 (t70) cc_final: 0.7112 (t0) REVERT: C 215 GLU cc_start: 0.7963 (mp0) cc_final: 0.7494 (mp0) REVERT: C 217 MET cc_start: 0.7496 (ppp) cc_final: 0.7183 (pmt) REVERT: C 325 MET cc_start: 0.8482 (tpp) cc_final: 0.8081 (tpp) REVERT: F 198 ARG cc_start: 0.7230 (ttm110) cc_final: 0.6571 (mtp85) REVERT: F 261 ASP cc_start: 0.7625 (m-30) cc_final: 0.6574 (t0) REVERT: F 273 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5305 (t80) REVERT: A 198 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7169 (tmm) REVERT: A 216 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: A 308 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7012 (mp0) outliers start: 64 outliers final: 25 residues processed: 152 average time/residue: 0.4342 time to fit residues: 71.4920 Evaluate side-chains 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 ASN R 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.203492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.140052 restraints weight = 9244.443| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.79 r_work: 0.3430 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8255 Z= 0.190 Angle : 0.676 11.283 11200 Z= 0.331 Chirality : 0.044 0.222 1289 Planarity : 0.004 0.057 1409 Dihedral : 6.006 58.494 1138 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 8.22 % Allowed : 27.08 % Favored : 64.70 % 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 aren not related in a simple way. whole: 0.11 (0.26), residues: 1017 helix: 1.75 (0.29), residues: 352 sheet: -0.07 (0.32), residues: 256 loop : -1.33 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.016 0.002 TYR C 59 PHE 0.022 0.002 PHE C 199 TRP 0.029 0.002 TRP R 105 HIS 0.005 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 8253) covalent geometry : angle 0.67619 (11196) SS BOND : bond 0.00491 ( 2) SS BOND : angle 1.11688 ( 4) hydrogen bonds : bond 0.04558 ( 379) hydrogen bonds : angle 4.50148 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 105 time to evaluate : 0.337 Fit side-chains REVERT: C 134 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7306 (ptt180) REVERT: C 199 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7371 (t80) REVERT: C 212 ASP cc_start: 0.7575 (t70) cc_final: 0.7084 (t0) REVERT: C 215 GLU cc_start: 0.7968 (mp0) cc_final: 0.7409 (mp0) REVERT: C 217 MET cc_start: 0.7559 (ppp) cc_final: 0.7222 (pmt) REVERT: C 325 MET cc_start: 0.8621 (tpp) cc_final: 0.8282 (tpp) REVERT: F 230 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7637 (ptp) REVERT: F 261 ASP cc_start: 0.7519 (m-30) cc_final: 0.6500 (t0) REVERT: F 273 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.5855 (t80) REVERT: R 223 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5812 (pt) REVERT: A 198 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7107 (tmm) REVERT: A 216 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: A 308 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7043 (mp0) outliers start: 71 outliers final: 34 residues processed: 159 average time/residue: 0.4479 time to fit residues: 76.9667 Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.0040 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.207675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140175 restraints weight = 9170.278| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.56 r_work: 0.3514 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8255 Z= 0.105 Angle : 0.601 10.328 11200 Z= 0.288 Chirality : 0.041 0.152 1289 Planarity : 0.004 0.049 1409 Dihedral : 5.588 57.353 1137 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % Rotamer: Outliers : 6.02 % Allowed : 28.82 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.27), residues: 1017 helix: 1.98 (0.29), residues: 347 sheet: -0.04 (0.32), residues: 250 loop : -1.23 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 198 TYR 0.014 0.001 TYR R 294 PHE 0.021 0.001 PHE R 306 TRP 0.032 0.001 TRP R 105 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8253) covalent geometry : angle 0.60142 (11196) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.63185 ( 4) hydrogen bonds : bond 0.03564 ( 379) hydrogen bonds : angle 4.29328 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 104 time to evaluate : 0.341 Fit side-chains REVERT: C 134 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7348 (ptt-90) REVERT: C 153 ASP cc_start: 0.7514 (m-30) cc_final: 0.7276 (m-30) REVERT: C 212 ASP cc_start: 0.7389 (t0) cc_final: 0.7086 (t0) REVERT: C 215 GLU cc_start: 0.7985 (mp0) cc_final: 0.7586 (mp0) REVERT: C 217 MET cc_start: 0.7499 (ppp) cc_final: 0.7162 (pmt) REVERT: C 232 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 270 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7862 (mp) REVERT: C 325 MET cc_start: 0.8495 (tpp) cc_final: 0.8104 (tpp) REVERT: F 198 ARG cc_start: 0.7177 (ttm110) cc_final: 0.6537 (mtp85) REVERT: F 230 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7580 (ptp) REVERT: F 261 ASP cc_start: 0.7669 (m-30) cc_final: 0.6647 (t0) REVERT: F 273 TYR cc_start: 0.5694 (OUTLIER) cc_final: 0.5104 (t80) REVERT: R 105 TRP cc_start: 0.5526 (t60) cc_final: 0.5215 (t60) REVERT: A 198 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7277 (tmm) REVERT: A 216 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: A 308 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7167 (mp0) outliers start: 52 outliers final: 23 residues processed: 143 average time/residue: 0.4740 time to fit residues: 73.0103 Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 ASN R 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.205331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134536 restraints weight = 9256.440| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.65 r_work: 0.3467 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8255 Z= 0.155 Angle : 0.652 12.704 11200 Z= 0.313 Chirality : 0.042 0.192 1289 Planarity : 0.004 0.056 1409 Dihedral : 5.455 56.562 1133 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 7.64 % Allowed : 27.78 % Favored : 64.58 % 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 aren not related in a simple way. whole: 0.20 (0.26), residues: 1017 helix: 1.93 (0.29), residues: 346 sheet: -0.06 (0.32), residues: 256 loop : -1.30 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 198 TYR 0.018 0.002 TYR R 294 PHE 0.022 0.002 PHE R 306 TRP 0.025 0.002 TRP R 105 HIS 0.004 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8253) covalent geometry : angle 0.65150 (11196) SS BOND : bond 0.00409 ( 2) SS BOND : angle 0.89797 ( 4) hydrogen bonds : bond 0.04086 ( 379) hydrogen bonds : angle 4.34787 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 103 time to evaluate : 0.338 Fit side-chains REVERT: C 18 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7620 (tp) REVERT: C 134 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7366 (ptt180) REVERT: C 212 ASP cc_start: 0.7482 (t0) cc_final: 0.7140 (t0) REVERT: C 215 GLU cc_start: 0.8015 (mp0) cc_final: 0.7581 (mp0) REVERT: C 217 MET cc_start: 0.7574 (ppp) cc_final: 0.7213 (pmt) REVERT: C 270 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7897 (mp) REVERT: C 325 MET cc_start: 0.8575 (tpp) cc_final: 0.8230 (tpp) REVERT: F 230 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7623 (ptp) REVERT: F 261 ASP cc_start: 0.7626 (m-30) cc_final: 0.6571 (t0) REVERT: F 273 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5515 (t80) REVERT: A 198 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7245 (tmm) REVERT: A 216 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: A 308 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7109 (mp0) outliers start: 66 outliers final: 34 residues processed: 155 average time/residue: 0.4359 time to fit residues: 73.2648 Evaluate side-chains 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 10.9990 chunk 86 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 ASN R 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.205435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.134708 restraints weight = 9261.139| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.66 r_work: 0.3472 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8255 Z= 0.149 Angle : 0.657 11.478 11200 Z= 0.315 Chirality : 0.042 0.191 1289 Planarity : 0.004 0.049 1409 Dihedral : 5.478 56.582 1133 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 7.41 % Allowed : 28.01 % Favored : 64.58 % 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 aren not related in a simple way. whole: 0.17 (0.26), residues: 1017 helix: 1.88 (0.29), residues: 347 sheet: -0.03 (0.32), residues: 250 loop : -1.33 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 198 TYR 0.020 0.002 TYR R 294 PHE 0.025 0.002 PHE R 306 TRP 0.035 0.002 TRP R 105 HIS 0.003 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8253) covalent geometry : angle 0.65714 (11196) SS BOND : bond 0.00365 ( 2) SS BOND : angle 0.83615 ( 4) hydrogen bonds : bond 0.04022 ( 379) hydrogen bonds : angle 4.35249 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 104 time to evaluate : 0.403 Fit side-chains REVERT: C 134 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7349 (ptt180) REVERT: C 212 ASP cc_start: 0.7525 (t0) cc_final: 0.7200 (t0) REVERT: C 215 GLU cc_start: 0.7994 (mp0) cc_final: 0.7587 (mp0) REVERT: C 217 MET cc_start: 0.7676 (ppp) cc_final: 0.7333 (pmt) REVERT: C 270 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7839 (mp) REVERT: C 325 MET cc_start: 0.8572 (tpp) cc_final: 0.8212 (tpp) REVERT: E 21 MET cc_start: 0.7064 (mpp) cc_final: 0.6766 (mpp) REVERT: F 198 ARG cc_start: 0.7162 (ttm110) cc_final: 0.6289 (mtm110) REVERT: F 230 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7630 (ptp) REVERT: F 261 ASP cc_start: 0.7607 (m-30) cc_final: 0.6560 (t0) REVERT: F 273 TYR cc_start: 0.6199 (OUTLIER) cc_final: 0.5475 (t80) REVERT: A 195 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.6033 (t-170) REVERT: A 198 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7274 (tmm) REVERT: A 216 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: A 308 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7134 (mp0) outliers start: 64 outliers final: 40 residues processed: 152 average time/residue: 0.4350 time to fit residues: 71.7134 Evaluate side-chains 148 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN F 115 ASN R 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.208613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138877 restraints weight = 9242.471| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.64 r_work: 0.3523 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8255 Z= 0.105 Angle : 0.621 13.100 11200 Z= 0.292 Chirality : 0.041 0.150 1289 Planarity : 0.004 0.055 1409 Dihedral : 4.920 58.040 1131 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.46 % Favored : 97.44 % Rotamer: Outliers : 6.25 % Allowed : 29.28 % Favored : 64.47 % 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 aren not related in a simple way. whole: 0.35 (0.27), residues: 1017 helix: 1.97 (0.29), residues: 346 sheet: 0.21 (0.33), residues: 243 loop : -1.23 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 198 TYR 0.018 0.001 TYR R 294 PHE 0.024 0.001 PHE R 306 TRP 0.045 0.001 TRP R 105 HIS 0.002 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8253) covalent geometry : angle 0.62076 (11196) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.66588 ( 4) hydrogen bonds : bond 0.03412 ( 379) hydrogen bonds : angle 4.20203 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 0.345 Fit side-chains REVERT: C 134 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7344 (ptt-90) REVERT: C 212 ASP cc_start: 0.7590 (t0) cc_final: 0.7243 (t0) REVERT: C 215 GLU cc_start: 0.7935 (mp0) cc_final: 0.7479 (mp0) REVERT: C 217 MET cc_start: 0.7595 (ppp) cc_final: 0.7252 (pmt) REVERT: C 232 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 270 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7821 (mp) REVERT: C 325 MET cc_start: 0.8518 (tpp) cc_final: 0.8102 (tpp) REVERT: E 21 MET cc_start: 0.7033 (mpp) cc_final: 0.6778 (mpp) REVERT: F 198 ARG cc_start: 0.7150 (ttm110) cc_final: 0.6511 (mtp85) REVERT: F 230 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7586 (ptp) REVERT: F 253 THR cc_start: 0.8278 (m) cc_final: 0.7991 (p) REVERT: F 261 ASP cc_start: 0.7701 (m-30) cc_final: 0.6574 (t0) REVERT: F 273 TYR cc_start: 0.5584 (OUTLIER) cc_final: 0.4922 (t80) REVERT: R 136 ASP cc_start: 0.6854 (t0) cc_final: 0.6593 (t0) REVERT: R 158 LEU cc_start: 0.4911 (pp) cc_final: 0.4370 (mt) REVERT: A 216 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: A 308 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7104 (mp0) outliers start: 54 outliers final: 25 residues processed: 152 average time/residue: 0.4630 time to fit residues: 76.1855 Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 ASN R 58 ASN A 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.206754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138215 restraints weight = 9160.828| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.58 r_work: 0.3490 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8255 Z= 0.131 Angle : 0.676 12.040 11200 Z= 0.317 Chirality : 0.042 0.168 1289 Planarity : 0.004 0.052 1409 Dihedral : 4.972 57.645 1131 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 5.90 % Allowed : 30.21 % Favored : 63.89 % 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 aren not related in a simple way. whole: 0.24 (0.27), residues: 1017 helix: 1.91 (0.29), residues: 347 sheet: 0.04 (0.32), residues: 252 loop : -1.28 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 198 TYR 0.024 0.001 TYR R 294 PHE 0.028 0.001 PHE R 306 TRP 0.053 0.002 TRP R 105 HIS 0.003 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8253) covalent geometry : angle 0.67606 (11196) SS BOND : bond 0.00329 ( 2) SS BOND : angle 0.81876 ( 4) hydrogen bonds : bond 0.03734 ( 379) hydrogen bonds : angle 4.22287 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 101 time to evaluate : 0.342 Fit side-chains REVERT: C 134 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7333 (ptt180) REVERT: C 212 ASP cc_start: 0.7585 (t0) cc_final: 0.7209 (t0) REVERT: C 215 GLU cc_start: 0.7944 (mp0) cc_final: 0.7436 (mp0) REVERT: C 217 MET cc_start: 0.7597 (ppp) cc_final: 0.7244 (pmt) REVERT: C 232 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8323 (mt) REVERT: C 270 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7819 (mp) REVERT: C 325 MET cc_start: 0.8559 (tpp) cc_final: 0.8213 (tpp) REVERT: F 115 ASN cc_start: 0.7887 (m-40) cc_final: 0.7653 (m-40) REVERT: F 198 ARG cc_start: 0.7129 (ttm110) cc_final: 0.6507 (mtp85) REVERT: F 230 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7598 (ptp) REVERT: F 253 THR cc_start: 0.8307 (m) cc_final: 0.8041 (p) REVERT: F 261 ASP cc_start: 0.7666 (m-30) cc_final: 0.6578 (t0) REVERT: F 273 TYR cc_start: 0.5836 (OUTLIER) cc_final: 0.5253 (t80) REVERT: R 136 ASP cc_start: 0.6850 (t0) cc_final: 0.6567 (t0) REVERT: R 158 LEU cc_start: 0.4891 (pp) cc_final: 0.4358 (mt) REVERT: A 216 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: A 266 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7460 (tt) REVERT: A 308 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7120 (mp0) outliers start: 51 outliers final: 33 residues processed: 142 average time/residue: 0.4796 time to fit residues: 73.4533 Evaluate side-chains 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 70 optimal weight: 0.0070 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN R 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.204039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136533 restraints weight = 9102.152| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.54 r_work: 0.3468 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8255 Z= 0.138 Angle : 0.687 11.641 11200 Z= 0.322 Chirality : 0.042 0.181 1289 Planarity : 0.004 0.054 1409 Dihedral : 4.968 57.285 1131 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.85 % Favored : 97.05 % Rotamer: Outliers : 5.56 % Allowed : 30.67 % Favored : 63.77 % 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 aren not related in a simple way. whole: 0.22 (0.27), residues: 1017 helix: 1.90 (0.29), residues: 348 sheet: 0.02 (0.32), residues: 252 loop : -1.30 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 198 TYR 0.025 0.002 TYR R 294 PHE 0.028 0.001 PHE R 306 TRP 0.055 0.002 TRP R 105 HIS 0.003 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8253) covalent geometry : angle 0.68715 (11196) SS BOND : bond 0.00356 ( 2) SS BOND : angle 0.96688 ( 4) hydrogen bonds : bond 0.03804 ( 379) hydrogen bonds : angle 4.23087 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 0.329 Fit side-chains REVERT: C 134 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7581 (ptt180) REVERT: C 212 ASP cc_start: 0.7744 (t0) cc_final: 0.7287 (t0) REVERT: C 215 GLU cc_start: 0.7952 (mp0) cc_final: 0.7374 (mp0) REVERT: C 232 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8356 (mt) REVERT: C 270 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7821 (mp) REVERT: C 325 MET cc_start: 0.8720 (tpp) cc_final: 0.8374 (tpp) REVERT: F 115 ASN cc_start: 0.7835 (m-40) cc_final: 0.7488 (m-40) REVERT: F 198 ARG cc_start: 0.7175 (ttm110) cc_final: 0.6462 (mtp85) REVERT: F 230 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7783 (ptp) REVERT: F 253 THR cc_start: 0.8277 (m) cc_final: 0.8007 (p) REVERT: F 261 ASP cc_start: 0.7608 (m-30) cc_final: 0.6489 (t0) REVERT: F 273 TYR cc_start: 0.6220 (OUTLIER) cc_final: 0.5597 (t80) REVERT: R 136 ASP cc_start: 0.7182 (t0) cc_final: 0.6905 (t0) REVERT: R 158 LEU cc_start: 0.4881 (pp) cc_final: 0.4345 (mt) REVERT: A 216 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: A 308 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7095 (mp0) outliers start: 48 outliers final: 33 residues processed: 136 average time/residue: 0.4633 time to fit residues: 68.0983 Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 8 TRP Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 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 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.205007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137760 restraints weight = 9115.777| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.53 r_work: 0.3490 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8255 Z= 0.122 Angle : 0.673 11.123 11200 Z= 0.313 Chirality : 0.042 0.162 1289 Planarity : 0.004 0.052 1409 Dihedral : 4.859 57.792 1131 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 5.44 % Allowed : 30.79 % Favored : 63.77 % 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 aren not related in a simple way. whole: 0.28 (0.27), residues: 1017 helix: 1.90 (0.29), residues: 348 sheet: 0.10 (0.33), residues: 250 loop : -1.24 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 198 TYR 0.023 0.001 TYR R 294 PHE 0.028 0.001 PHE R 306 TRP 0.060 0.002 TRP R 105 HIS 0.003 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8253) covalent geometry : angle 0.67285 (11196) SS BOND : bond 0.00313 ( 2) SS BOND : angle 0.85042 ( 4) hydrogen bonds : bond 0.03591 ( 379) hydrogen bonds : angle 4.18822 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3494.47 seconds wall clock time: 60 minutes 23.77 seconds (3623.77 seconds total)