Starting phenix.real_space_refine on Sun May 11 11:01:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4o_36888/05_2025/8k4o_36888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4o_36888/05_2025/8k4o_36888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k4o_36888/05_2025/8k4o_36888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4o_36888/05_2025/8k4o_36888.map" model { file = "/net/cci-nas-00/data/ceres_data/8k4o_36888/05_2025/8k4o_36888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4o_36888/05_2025/8k4o_36888.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.092 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 60 5.16 5 C 5054 2.51 5 N 1369 2.21 5 O 1463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7946 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2664 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 7, 'TRANS': 325} Chain: "F" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 467 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2572 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1825 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 226} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Time building chain proxies: 4.83, per 1000 atoms: 0.61 Number of scatterers: 7946 At special positions: 0 Unit cell: (74.8, 102.85, 164.9, 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 60 16.00 O 1463 8.00 N 1369 7.00 C 5054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 118 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 35 " distance=2.03 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.0 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 38.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'E' and resid 46 through 75 removed outlier: 3.792A pdb=" N ASN E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.951A pdb=" N ILE E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER E 99 " --> pdb=" O CYS E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 110 through 113 removed outlier: 3.807A pdb=" N ILE E 113 " --> pdb=" O PRO E 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'E' and resid 114 through 149 removed outlier: 3.599A pdb=" N ARG E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 120 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP E 132 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE E 133 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS E 138 " --> pdb=" O PHE E 134 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 156 Processing helix chain 'E' and resid 157 through 180 removed outlier: 3.919A pdb=" N GLY E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 removed outlier: 4.136A pdb=" N MET E 203 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 204 " --> pdb=" O GLY E 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 204' Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.649A pdb=" N ARG E 212 " --> pdb=" O ARG E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 239 removed outlier: 3.615A pdb=" N THR E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 279 removed outlier: 3.617A pdb=" N ALA E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Proline residue: E 266 - end of helix removed outlier: 3.548A pdb=" N ASN E 271 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 272 " --> pdb=" O HIS E 268 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 309 removed outlier: 3.824A pdb=" N ALA E 297 " --> pdb=" O ASN E 293 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 317 removed outlier: 3.577A pdb=" N LEU E 317 " --> pdb=" O ILE E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.770A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 63 removed outlier: 3.742A pdb=" N ILE F 62 " --> pdb=" O ILE F 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 removed outlier: 3.766A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'C' and resid 9 through 12 Processing helix chain 'C' and resid 13 through 30 removed outlier: 3.611A pdb=" N LYS C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 removed outlier: 3.681A pdb=" N LYS C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 removed outlier: 3.652A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 216 " --> pdb=" O HIS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.790A pdb=" N ASN C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.523A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.715A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 331 through 352 removed outlier: 3.574A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'E' and resid 183 through 187 Processing sheet with id=AA2, first strand: chain 'F' and resid 25 through 28 removed outlier: 3.594A pdb=" N LEU F 44 " --> pdb=" O ARG F 48 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.862A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.624A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.908A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.093A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.600A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.012A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 185 removed outlier: 3.605A pdb=" N ASP C 200 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 201 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 38 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 190 removed outlier: 6.147A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 201 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 38 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2581 1.34 - 1.46: 1354 1.46 - 1.58: 4079 1.58 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8096 Sorted by residual: bond pdb=" CA ARG E 283 " pdb=" C ARG E 283 " ideal model delta sigma weight residual 1.523 1.470 0.054 1.32e-02 5.74e+03 1.65e+01 bond pdb=" C THR G 52 " pdb=" O THR G 52 " ideal model delta sigma weight residual 1.246 1.229 0.017 9.20e-03 1.18e+04 3.51e+00 bond pdb=" CA LEU G 50 " pdb=" C LEU G 50 " ideal model delta sigma weight residual 1.523 1.501 0.023 1.34e-02 5.57e+03 2.82e+00 bond pdb=" CA LEU G 51 " pdb=" C LEU G 51 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.30e-02 5.92e+03 1.60e+00 bond pdb=" C SER F 56 " pdb=" N PRO F 57 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.48e+00 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 10747 1.77 - 3.53: 173 3.53 - 5.30: 37 5.30 - 7.07: 7 7.07 - 8.84: 1 Bond angle restraints: 10965 Sorted by residual: angle pdb=" C CYS C 325 " pdb=" CA CYS C 325 " pdb=" CB CYS C 325 " ideal model delta sigma weight residual 116.54 109.59 6.95 1.15e+00 7.56e-01 3.65e+01 angle pdb=" N LEU G 51 " pdb=" CA LEU G 51 " pdb=" C LEU G 51 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" N VAL E 147 " pdb=" CA VAL E 147 " pdb=" C VAL E 147 " ideal model delta sigma weight residual 112.96 108.53 4.43 1.00e+00 1.00e+00 1.96e+01 angle pdb=" CA CYS C 325 " pdb=" C CYS C 325 " pdb=" N ALA C 326 " ideal model delta sigma weight residual 119.52 116.56 2.96 7.90e-01 1.60e+00 1.41e+01 angle pdb=" N PRO G 60 " pdb=" CA PRO G 60 " pdb=" C PRO G 60 " ideal model delta sigma weight residual 113.65 109.22 4.43 1.35e+00 5.49e-01 1.07e+01 ... (remaining 10960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4073 17.32 - 34.64: 565 34.64 - 51.96: 163 51.96 - 69.28: 38 69.28 - 86.60: 5 Dihedral angle restraints: 4844 sinusoidal: 1889 harmonic: 2955 Sorted by residual: dihedral pdb=" CA SER B 67 " pdb=" C SER B 67 " pdb=" N ARG B 68 " pdb=" CA ARG B 68 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TRP E 207 " pdb=" C TRP E 207 " pdb=" N ARG E 208 " pdb=" CA ARG E 208 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP C 237 " pdb=" C ASP C 237 " pdb=" N GLU C 238 " pdb=" CA GLU C 238 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 4841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 711 0.026 - 0.052: 338 0.052 - 0.078: 133 0.078 - 0.104: 51 0.104 - 0.129: 38 Chirality restraints: 1271 Sorted by residual: chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CB THR B 87 " pdb=" CA THR B 87 " pdb=" OG1 THR B 87 " pdb=" CG2 THR B 87 " both_signs ideal model delta sigma weight residual False 2.55 2.68 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1268 not shown) Planarity restraints: 1382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 32 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO F 33 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 33 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 33 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 163 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" CG ASP B 163 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP B 163 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 163 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 281 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 282 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 282 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 282 " -0.025 5.00e-02 4.00e+02 ... (remaining 1379 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 347 2.72 - 3.26: 7629 3.26 - 3.81: 11975 3.81 - 4.35: 15035 4.35 - 4.90: 26647 Nonbonded interactions: 61633 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.169 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.252 3.040 nonbonded pdb=" O GLU B 12 " pdb=" ND2 ASN B 16 " model vdw 2.269 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.274 3.040 nonbonded pdb=" N ASP B 186 " pdb=" OD1 ASP B 186 " model vdw 2.277 3.120 ... (remaining 61628 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.590 Find NCS groups from input model: 0.090 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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 0.054 8099 Z= 0.136 Angle : 0.585 8.836 10971 Z= 0.334 Chirality : 0.040 0.129 1271 Planarity : 0.004 0.088 1382 Dihedral : 17.481 86.602 2921 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 6.21 % Allowed : 30.26 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.26), residues: 1002 helix: 0.33 (0.27), residues: 393 sheet: -0.33 (0.36), residues: 184 loop : -2.05 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS E 268 PHE 0.012 0.001 PHE B 241 TYR 0.009 0.001 TYR E 128 ARG 0.005 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.14747 ( 322) hydrogen bonds : angle 5.34844 ( 936) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.45426 ( 6) covalent geometry : bond 0.00276 ( 8096) covalent geometry : angle 0.58511 (10965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 103 time to evaluate : 0.921 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: C 273 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8548 (tt) outliers start: 54 outliers final: 52 residues processed: 155 average time/residue: 0.1884 time to fit residues: 40.2637 Evaluate side-chains 156 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 103 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101837 restraints weight = 9630.550| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.48 r_work: 0.2980 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8099 Z= 0.185 Angle : 0.583 6.085 10971 Z= 0.314 Chirality : 0.043 0.140 1271 Planarity : 0.004 0.068 1382 Dihedral : 9.214 74.508 1177 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.33 % Allowed : 27.96 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.26), residues: 1002 helix: 0.42 (0.28), residues: 389 sheet: -0.35 (0.37), residues: 182 loop : -2.14 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.014 0.002 PHE B 241 TYR 0.014 0.001 TYR E 128 ARG 0.003 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.05102 ( 322) hydrogen bonds : angle 4.35142 ( 936) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.58378 ( 6) covalent geometry : bond 0.00441 ( 8096) covalent geometry : angle 0.58298 (10965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 0.872 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 182 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8398 (m170) REVERT: E 289 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7584 (ptt180) REVERT: B 163 ASP cc_start: 0.7601 (t0) cc_final: 0.7378 (t0) REVERT: C 23 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7375 (mp) REVERT: C 26 ASP cc_start: 0.8356 (m-30) cc_final: 0.8090 (m-30) REVERT: C 33 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: C 273 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8298 (tt) REVERT: G 9 ILE cc_start: 0.4488 (OUTLIER) cc_final: 0.4099 (pp) outliers start: 55 outliers final: 32 residues processed: 156 average time/residue: 0.1954 time to fit residues: 41.5440 Evaluate side-chains 137 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.0570 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.154964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105743 restraints weight = 9597.756| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.64 r_work: 0.3034 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8099 Z= 0.101 Angle : 0.500 5.473 10971 Z= 0.271 Chirality : 0.040 0.131 1271 Planarity : 0.004 0.059 1382 Dihedral : 7.889 73.336 1139 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.72 % Allowed : 29.46 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 1002 helix: 0.81 (0.28), residues: 387 sheet: -0.26 (0.37), residues: 184 loop : -2.02 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.000 HIS E 268 PHE 0.010 0.001 PHE C 189 TYR 0.008 0.001 TYR E 128 ARG 0.002 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 322) hydrogen bonds : angle 4.02272 ( 936) SS BOND : bond 0.00151 ( 3) SS BOND : angle 0.39876 ( 6) covalent geometry : bond 0.00221 ( 8096) covalent geometry : angle 0.50003 (10965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.829 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 70 TYR cc_start: 0.8441 (t80) cc_final: 0.8147 (t80) REVERT: E 182 HIS cc_start: 0.8839 (OUTLIER) cc_final: 0.8394 (m170) REVERT: B 22 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6913 (ttm-80) REVERT: C 26 ASP cc_start: 0.8337 (m-30) cc_final: 0.8062 (m-30) REVERT: C 273 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8315 (tt) REVERT: G 9 ILE cc_start: 0.4506 (OUTLIER) cc_final: 0.4064 (pp) outliers start: 41 outliers final: 27 residues processed: 144 average time/residue: 0.2017 time to fit residues: 39.5726 Evaluate side-chains 135 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 182 HIS Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103719 restraints weight = 9629.579| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.63 r_work: 0.3011 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8099 Z= 0.127 Angle : 0.508 5.509 10971 Z= 0.275 Chirality : 0.041 0.134 1271 Planarity : 0.004 0.055 1382 Dihedral : 7.420 75.511 1129 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 5.87 % Allowed : 27.50 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1002 helix: 0.86 (0.28), residues: 390 sheet: -0.25 (0.37), residues: 183 loop : -2.05 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS E 268 PHE 0.012 0.001 PHE B 241 TYR 0.011 0.001 TYR B 111 ARG 0.003 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 322) hydrogen bonds : angle 3.93531 ( 936) SS BOND : bond 0.00103 ( 3) SS BOND : angle 0.38711 ( 6) covalent geometry : bond 0.00295 ( 8096) covalent geometry : angle 0.50772 (10965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 0.885 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 70 TYR cc_start: 0.8446 (t80) cc_final: 0.8150 (t80) REVERT: E 209 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (tt) REVERT: B 57 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8624 (mttt) REVERT: B 82 TRP cc_start: 0.9121 (OUTLIER) cc_final: 0.8896 (m100) REVERT: B 163 ASP cc_start: 0.7321 (t0) cc_final: 0.7053 (t0) REVERT: B 314 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8071 (mtt180) REVERT: B 323 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8134 (p0) REVERT: C 23 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7431 (mp) REVERT: C 26 ASP cc_start: 0.8327 (m-30) cc_final: 0.8045 (m-30) REVERT: C 33 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: C 273 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8288 (tt) REVERT: G 9 ILE cc_start: 0.4426 (OUTLIER) cc_final: 0.4010 (pp) outliers start: 51 outliers final: 30 residues processed: 156 average time/residue: 0.1938 time to fit residues: 41.0096 Evaluate side-chains 145 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108943 restraints weight = 9422.333| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.72 r_work: 0.3092 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8099 Z= 0.100 Angle : 0.477 5.397 10971 Z= 0.259 Chirality : 0.040 0.130 1271 Planarity : 0.003 0.051 1382 Dihedral : 7.138 75.576 1128 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.72 % Allowed : 28.88 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 1002 helix: 1.02 (0.29), residues: 391 sheet: -0.12 (0.38), residues: 179 loop : -2.02 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS E 268 PHE 0.012 0.001 PHE E 107 TYR 0.009 0.001 TYR E 128 ARG 0.003 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 322) hydrogen bonds : angle 3.80922 ( 936) SS BOND : bond 0.00089 ( 3) SS BOND : angle 0.34793 ( 6) covalent geometry : bond 0.00224 ( 8096) covalent geometry : angle 0.47686 (10965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.841 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 70 TYR cc_start: 0.8383 (t80) cc_final: 0.8093 (t80) REVERT: B 22 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6972 (ttm-80) REVERT: B 57 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8594 (mttt) REVERT: B 82 TRP cc_start: 0.9054 (OUTLIER) cc_final: 0.8816 (m100) REVERT: B 163 ASP cc_start: 0.7095 (t0) cc_final: 0.6784 (t0) REVERT: B 314 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8038 (mtt180) REVERT: C 26 ASP cc_start: 0.8229 (m-30) cc_final: 0.7933 (m-30) REVERT: C 33 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: C 273 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8248 (tt) REVERT: G 9 ILE cc_start: 0.4317 (OUTLIER) cc_final: 0.3892 (pp) REVERT: G 48 ASP cc_start: 0.8530 (t0) cc_final: 0.8255 (t0) outliers start: 41 outliers final: 28 residues processed: 143 average time/residue: 0.2069 time to fit residues: 39.6450 Evaluate side-chains 143 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106108 restraints weight = 9412.801| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.77 r_work: 0.3054 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8099 Z= 0.133 Angle : 0.539 15.664 10971 Z= 0.280 Chirality : 0.041 0.241 1271 Planarity : 0.003 0.050 1382 Dihedral : 6.856 77.579 1124 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 5.52 % Allowed : 28.08 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 1002 helix: 1.00 (0.29), residues: 391 sheet: -0.24 (0.37), residues: 186 loop : -2.04 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS E 268 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR B 111 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 322) hydrogen bonds : angle 3.85022 ( 936) SS BOND : bond 0.00110 ( 3) SS BOND : angle 0.38469 ( 6) covalent geometry : bond 0.00315 ( 8096) covalent geometry : angle 0.53904 (10965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 0.945 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4154 (pt0) REVERT: E 70 TYR cc_start: 0.8406 (t80) cc_final: 0.8111 (t80) REVERT: B 22 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6969 (ttm-80) REVERT: B 57 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8605 (mttt) REVERT: B 163 ASP cc_start: 0.7235 (t0) cc_final: 0.6937 (t0) REVERT: B 314 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8051 (mtt180) REVERT: C 23 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7283 (mp) REVERT: C 33 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: C 273 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8241 (tt) REVERT: G 9 ILE cc_start: 0.4191 (OUTLIER) cc_final: 0.3814 (pp) REVERT: G 48 ASP cc_start: 0.8632 (t0) cc_final: 0.8409 (t0) outliers start: 48 outliers final: 29 residues processed: 148 average time/residue: 0.2188 time to fit residues: 43.1221 Evaluate side-chains 142 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 0.0030 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108069 restraints weight = 9462.249| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.84 r_work: 0.3087 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8099 Z= 0.099 Angle : 0.504 15.629 10971 Z= 0.262 Chirality : 0.040 0.222 1271 Planarity : 0.003 0.048 1382 Dihedral : 6.573 77.275 1122 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.60 % Allowed : 28.77 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 1002 helix: 1.11 (0.29), residues: 391 sheet: -0.19 (0.38), residues: 174 loop : -1.99 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS E 268 PHE 0.011 0.001 PHE E 107 TYR 0.009 0.001 TYR E 128 ARG 0.006 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 322) hydrogen bonds : angle 3.75078 ( 936) SS BOND : bond 0.00085 ( 3) SS BOND : angle 0.33698 ( 6) covalent geometry : bond 0.00220 ( 8096) covalent geometry : angle 0.50386 (10965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.4935 (OUTLIER) cc_final: 0.4036 (pt0) REVERT: E 70 TYR cc_start: 0.8340 (t80) cc_final: 0.8033 (t80) REVERT: B 17 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 57 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8527 (mttt) REVERT: B 163 ASP cc_start: 0.6884 (t0) cc_final: 0.6552 (t0) REVERT: B 314 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7954 (mtt180) REVERT: C 23 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7252 (mp) REVERT: C 273 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8291 (tt) REVERT: G 9 ILE cc_start: 0.4450 (OUTLIER) cc_final: 0.4052 (pp) outliers start: 40 outliers final: 30 residues processed: 144 average time/residue: 0.2227 time to fit residues: 42.5209 Evaluate side-chains 143 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103136 restraints weight = 9552.850| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.70 r_work: 0.3042 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8099 Z= 0.157 Angle : 0.556 16.537 10971 Z= 0.289 Chirality : 0.042 0.209 1271 Planarity : 0.004 0.049 1382 Dihedral : 6.700 80.634 1120 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 5.18 % Allowed : 28.31 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1002 helix: 0.96 (0.28), residues: 391 sheet: -0.18 (0.37), residues: 181 loop : -2.08 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS E 268 PHE 0.014 0.001 PHE B 241 TYR 0.015 0.001 TYR B 111 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 322) hydrogen bonds : angle 3.89256 ( 936) SS BOND : bond 0.00119 ( 3) SS BOND : angle 0.42657 ( 6) covalent geometry : bond 0.00378 ( 8096) covalent geometry : angle 0.55630 (10965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 0.926 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.5035 (OUTLIER) cc_final: 0.4147 (pt0) REVERT: E 70 TYR cc_start: 0.8404 (t80) cc_final: 0.8101 (t80) REVERT: B 17 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 57 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8600 (mttt) REVERT: B 163 ASP cc_start: 0.7275 (t0) cc_final: 0.6975 (t0) REVERT: B 314 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8167 (mtt180) REVERT: C 23 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7274 (mp) REVERT: C 33 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: C 273 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8237 (tt) REVERT: G 9 ILE cc_start: 0.4349 (OUTLIER) cc_final: 0.3972 (pp) outliers start: 45 outliers final: 32 residues processed: 144 average time/residue: 0.2101 time to fit residues: 40.4826 Evaluate side-chains 142 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107527 restraints weight = 9572.258| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.82 r_work: 0.3075 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8099 Z= 0.100 Angle : 0.509 16.060 10971 Z= 0.264 Chirality : 0.040 0.207 1271 Planarity : 0.003 0.047 1382 Dihedral : 6.528 79.077 1120 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.37 % Allowed : 29.23 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 1002 helix: 1.12 (0.29), residues: 391 sheet: -0.18 (0.37), residues: 186 loop : -2.05 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS E 268 PHE 0.012 0.001 PHE E 107 TYR 0.008 0.001 TYR E 128 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 322) hydrogen bonds : angle 3.75728 ( 936) SS BOND : bond 0.00072 ( 3) SS BOND : angle 0.33748 ( 6) covalent geometry : bond 0.00222 ( 8096) covalent geometry : angle 0.50920 (10965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.4997 (OUTLIER) cc_final: 0.4122 (pt0) REVERT: E 70 TYR cc_start: 0.8339 (t80) cc_final: 0.8034 (t80) REVERT: B 57 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8524 (mttt) REVERT: B 163 ASP cc_start: 0.6800 (t0) cc_final: 0.6528 (t0) REVERT: B 314 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7953 (mtt180) REVERT: C 273 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8295 (tt) REVERT: G 9 ILE cc_start: 0.4443 (OUTLIER) cc_final: 0.4045 (pp) outliers start: 38 outliers final: 30 residues processed: 136 average time/residue: 0.2257 time to fit residues: 41.0237 Evaluate side-chains 137 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100589 restraints weight = 9540.182| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.49 r_work: 0.3049 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8099 Z= 0.168 Angle : 0.570 17.061 10971 Z= 0.296 Chirality : 0.042 0.201 1271 Planarity : 0.004 0.049 1382 Dihedral : 6.725 82.730 1120 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.49 % Allowed : 29.23 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1002 helix: 0.96 (0.28), residues: 391 sheet: -0.19 (0.37), residues: 181 loop : -2.08 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS E 268 PHE 0.015 0.002 PHE B 241 TYR 0.017 0.001 TYR B 111 ARG 0.006 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 322) hydrogen bonds : angle 3.88557 ( 936) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.38458 ( 6) covalent geometry : bond 0.00406 ( 8096) covalent geometry : angle 0.57049 (10965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.908 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 19 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.4176 (pt0) REVERT: E 178 ASP cc_start: 0.8823 (t0) cc_final: 0.8620 (t0) REVERT: B 57 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8626 (mttt) REVERT: B 163 ASP cc_start: 0.7260 (t0) cc_final: 0.7007 (t0) REVERT: B 314 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8213 (mtt180) REVERT: C 23 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7351 (mp) REVERT: C 273 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8258 (tt) REVERT: G 9 ILE cc_start: 0.4207 (OUTLIER) cc_final: 0.3821 (pp) outliers start: 39 outliers final: 30 residues processed: 137 average time/residue: 0.2221 time to fit residues: 40.7666 Evaluate side-chains 138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 289 ARG Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 19 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 0.0370 chunk 69 optimal weight: 7.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108884 restraints weight = 9503.645| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.69 r_work: 0.3079 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8099 Z= 0.102 Angle : 0.521 16.189 10971 Z= 0.270 Chirality : 0.041 0.204 1271 Planarity : 0.003 0.047 1382 Dihedral : 6.565 81.168 1120 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.26 % Allowed : 29.46 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.27), residues: 1002 helix: 1.08 (0.29), residues: 394 sheet: -0.22 (0.37), residues: 186 loop : -1.98 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS E 268 PHE 0.011 0.001 PHE E 107 TYR 0.011 0.001 TYR C 287 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 322) hydrogen bonds : angle 3.75028 ( 936) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.27964 ( 6) covalent geometry : bond 0.00229 ( 8096) covalent geometry : angle 0.52061 (10965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4989.11 seconds wall clock time: 86 minutes 51.34 seconds (5211.34 seconds total)