Starting phenix.real_space_refine on Mon Apr 28 19:06:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4o_36888/04_2025/8k4o_36888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4o_36888/04_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_36888/04_2025/8k4o_36888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4o_36888/04_2025/8k4o_36888.map" model { file = "/net/cci-nas-00/data/ceres_data/8k4o_36888/04_2025/8k4o_36888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4o_36888/04_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-5669/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: 5.09, per 1000 atoms: 0.64 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: 1.71 Conformation dependent library (CDL) restraints added in 1.2 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: 0.91 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: 2.08 Time building geometry restraints manager: 2.07 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.230 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- 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 : 0.819 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: 0.1873 time to fit residues: 39.8976 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 : 0.907 ------------------------------------------------------------------------------- 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 = 9630.549| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.48 r_work: 0.2980 rms_B_bonded: 3.11 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 : 0.909 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 182 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.8399 (m170) REVERT: E 289 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7587 (ptt180) REVERT: B 163 ASP cc_start: 0.7600 (t0) cc_final: 0.7378 (t0) REVERT: C 23 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7374 (mp) REVERT: C 26 ASP cc_start: 0.8357 (m-30) cc_final: 0.8091 (m-30) REVERT: C 33 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: C 273 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8300 (tt) REVERT: G 9 ILE cc_start: 0.4505 (OUTLIER) cc_final: 0.4110 (pp) outliers start: 55 outliers final: 32 residues processed: 156 average time/residue: 0.1908 time to fit residues: 40.5345 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 : 0.816 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.155013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105639 restraints weight = 9602.820| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.68 r_work: 0.3011 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1003 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= 0.101 Angle : 0.499 5.463 10971 Z= 0.270 Chirality : 0.040 0.131 1271 Planarity : 0.004 0.059 1382 Dihedral : 7.862 73.419 1139 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.83 % Allowed : 29.34 % 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: 0.82 (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 B 91 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 0.03706 ( 322) hydrogen bonds : angle 4.00954 ( 936) SS BOND : bond 0.00157 ( 3) SS BOND : angle 0.40517 ( 6) covalent geometry : bond 0.00222 ( 8096) covalent geometry : angle 0.49867 (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 153 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 1.028 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: 0.8443 (t80) cc_final: 0.8147 (t80) REVERT: E 182 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8386 (m170) REVERT: B 22 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6905 (ttm-80) REVERT: B 323 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8009 (p0) REVERT: C 26 ASP cc_start: 0.8341 (m-30) cc_final: 0.8058 (m-30) REVERT: C 273 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8303 (tt) REVERT: G 9 ILE cc_start: 0.4506 (OUTLIER) cc_final: 0.4060 (pp) REVERT: G 51 LEU cc_start: 0.8809 (tp) cc_final: 0.8605 (tp) outliers start: 42 outliers final: 27 residues processed: 144 average time/residue: 0.2058 time to fit residues: 40.2370 Evaluate side-chains 137 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 112 VAL 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: 0.8980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.151866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104020 restraints weight = 9631.338| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.50 r_work: 0.3003 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8099 Z= 0.129 Angle : 0.510 5.522 10971 Z= 0.276 Chirality : 0.041 0.135 1271 Planarity : 0.004 0.055 1382 Dihedral : 7.424 75.747 1129 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.64 % Allowed : 27.62 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.28), residues: 390 sheet: -0.26 (0.37), residues: 183 loop : -2.06 (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 0.012 0.001 TYR B 111 ARG 0.003 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 322) hydrogen bonds : angle 3.94431 ( 936) SS BOND : bond 0.00100 ( 3) SS BOND : angle 0.39239 ( 6) covalent geometry : bond 0.00303 ( 8096) covalent geometry : angle 0.50980 (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 163 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 0.848 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 70 TYR cc_start: 0.8437 (t80) cc_final: 0.8134 (t80) REVERT: E 209 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8433 (tt) REVERT: B 57 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8626 (mttt) REVERT: B 82 TRP cc_start: 0.9123 (OUTLIER) cc_final: 0.8902 (m100) REVERT: B 163 ASP cc_start: 0.7339 (t0) cc_final: 0.7081 (t0) REVERT: B 314 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8071 (mtt180) REVERT: B 323 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8145 (p0) REVERT: C 23 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7402 (mp) REVERT: C 26 ASP cc_start: 0.8322 (m-30) cc_final: 0.8039 (m-30) REVERT: C 33 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: C 273 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8302 (tt) REVERT: G 9 ILE cc_start: 0.4408 (OUTLIER) cc_final: 0.3995 (pp) outliers start: 49 outliers final: 30 residues processed: 155 average time/residue: 0.2203 time to fit residues: 45.8026 Evaluate side-chains 146 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.158168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108280 restraints weight = 9422.904| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.82 r_work: 0.3085 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8099 Z= 0.100 Angle : 0.477 5.384 10971 Z= 0.259 Chirality : 0.040 0.130 1271 Planarity : 0.003 0.051 1382 Dihedral : 7.149 75.598 1128 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.83 % Allowed : 28.65 % 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: -0.70 (0.27), residues: 1002 helix: 1.01 (0.29), residues: 391 sheet: -0.18 (0.38), residues: 178 loop : -2.03 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS C 213 PHE 0.012 0.001 PHE E 107 TYR 0.009 0.001 TYR E 128 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 322) hydrogen bonds : angle 3.82077 ( 936) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.32470 ( 6) covalent geometry : bond 0.00223 ( 8096) covalent geometry : angle 0.47660 (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 155 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.849 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: 0.8294 (t80) cc_final: 0.7986 (t80) REVERT: B 17 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 22 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6995 (ttm-80) REVERT: B 57 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8470 (mttt) REVERT: B 82 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.8722 (m100) REVERT: B 163 ASP cc_start: 0.6890 (t0) cc_final: 0.6587 (t0) REVERT: B 314 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7911 (mtt180) REVERT: C 26 ASP cc_start: 0.8052 (m-30) cc_final: 0.7740 (m-30) REVERT: C 273 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8235 (tt) REVERT: G 9 ILE cc_start: 0.4285 (OUTLIER) cc_final: 0.3884 (pp) REVERT: G 48 ASP cc_start: 0.8404 (t0) cc_final: 0.8203 (t0) outliers start: 42 outliers final: 29 residues processed: 147 average time/residue: 0.2072 time to fit residues: 40.7623 Evaluate side-chains 145 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 146 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.0980 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: 5.9990 chunk 66 optimal weight: 0.6980 chunk 80 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.158971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108319 restraints weight = 9376.029| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.84 r_work: 0.3093 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1439 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= 0.095 Angle : 0.506 15.046 10971 Z= 0.262 Chirality : 0.040 0.235 1271 Planarity : 0.003 0.049 1382 Dihedral : 6.768 75.477 1125 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.83 % Allowed : 28.77 % 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: -0.59 (0.27), residues: 1002 helix: 1.15 (0.29), residues: 391 sheet: -0.14 (0.39), residues: 172 loop : -1.98 (0.26), residues: 439 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 0.008 0.001 TYR E 128 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 322) hydrogen bonds : angle 3.74752 ( 936) SS BOND : bond 0.00078 ( 3) SS BOND : angle 0.28985 ( 6) covalent geometry : bond 0.00210 ( 8096) covalent geometry : angle 0.50623 (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: 42 poor density : 114 time to evaluate : 0.992 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: 0.5099 (OUTLIER) cc_final: 0.4213 (pt0) REVERT: E 70 TYR cc_start: 0.8333 (t80) cc_final: 0.8023 (t80) REVERT: B 17 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 57 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8527 (mttt) REVERT: B 82 TRP cc_start: 0.8957 (OUTLIER) cc_final: 0.8736 (m100) REVERT: B 163 ASP cc_start: 0.6853 (t0) cc_final: 0.6529 (t0) REVERT: B 314 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7966 (mtt180) REVERT: C 23 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7282 (mp) REVERT: C 26 ASP cc_start: 0.8059 (m-30) cc_final: 0.7772 (m-30) REVERT: C 33 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: C 273 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8288 (tt) REVERT: G 9 ILE cc_start: 0.4411 (OUTLIER) cc_final: 0.4023 (pp) outliers start: 42 outliers final: 28 residues processed: 149 average time/residue: 0.2020 time to fit residues: 40.3618 Evaluate side-chains 147 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 19 HIS 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 146 LEU 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 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: 0.7980 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.154217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102717 restraints weight = 9563.687| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.42 r_work: 0.3050 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8099 Z= 0.130 Angle : 0.534 15.995 10971 Z= 0.278 Chirality : 0.041 0.216 1271 Planarity : 0.004 0.049 1382 Dihedral : 6.809 78.431 1124 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.72 % Allowed : 29.00 % 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: -0.66 (0.27), residues: 1002 helix: 1.06 (0.29), residues: 391 sheet: -0.20 (0.37), residues: 186 loop : -2.04 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS E 268 PHE 0.013 0.001 PHE B 241 TYR 0.011 0.001 TYR E 128 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 322) hydrogen bonds : angle 3.83149 ( 936) SS BOND : bond 0.00110 ( 3) SS BOND : angle 0.38911 ( 6) covalent geometry : bond 0.00307 ( 8096) covalent geometry : angle 0.53398 (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: 41 poor density : 110 time to evaluate : 0.797 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: 0.8415 (t80) cc_final: 0.8104 (t80) REVERT: B 17 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 57 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8604 (mttt) REVERT: B 163 ASP cc_start: 0.7177 (t0) cc_final: 0.6872 (t0) REVERT: B 314 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8089 (mtt180) REVERT: C 23 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7333 (mp) REVERT: C 26 ASP cc_start: 0.8231 (m-30) cc_final: 0.7931 (m-30) REVERT: C 33 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: C 273 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8282 (tt) REVERT: G 9 ILE cc_start: 0.4238 (OUTLIER) cc_final: 0.3856 (pp) outliers start: 41 outliers final: 27 residues processed: 145 average time/residue: 0.2184 time to fit residues: 42.3319 Evaluate side-chains 141 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR 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 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 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=2.00 ------------------------------------------------------------------------------- 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: 0.6980 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.150101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097948 restraints weight = 9635.256| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.52 r_work: 0.3012 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8099 Z= 0.252 Angle : 0.632 16.847 10971 Z= 0.330 Chirality : 0.045 0.201 1271 Planarity : 0.004 0.051 1382 Dihedral : 7.153 84.547 1122 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % 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: -1.03 (0.26), residues: 1002 helix: 0.68 (0.28), residues: 392 sheet: -0.33 (0.37), residues: 181 loop : -2.18 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS C 213 PHE 0.017 0.002 PHE B 241 TYR 0.021 0.002 TYR B 111 ARG 0.008 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.05549 ( 322) hydrogen bonds : angle 4.12207 ( 936) SS BOND : bond 0.00159 ( 3) SS BOND : angle 0.59730 ( 6) covalent geometry : bond 0.00622 ( 8096) covalent geometry : angle 0.63250 (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 150 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.923 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 289 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7570 (ptt180) REVERT: B 57 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8648 (mttt) REVERT: B 66 ASP cc_start: 0.8304 (p0) cc_final: 0.8073 (p0) REVERT: B 163 ASP cc_start: 0.7547 (t0) cc_final: 0.7292 (t0) REVERT: B 314 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8274 (mtt180) REVERT: C 23 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7457 (mp) REVERT: C 26 ASP cc_start: 0.8336 (m-30) cc_final: 0.8031 (m-30) REVERT: C 33 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: C 273 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8288 (tt) REVERT: G 9 ILE cc_start: 0.4442 (OUTLIER) cc_final: 0.4076 (pp) outliers start: 41 outliers final: 29 residues processed: 143 average time/residue: 0.2098 time to fit residues: 40.4248 Evaluate side-chains 141 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE 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 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 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE 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 253 ILE 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: 6.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.154316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105416 restraints weight = 9624.427| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.75 r_work: 0.3061 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1502 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= 0.110 Angle : 0.535 16.134 10971 Z= 0.279 Chirality : 0.041 0.213 1271 Planarity : 0.003 0.049 1382 Dihedral : 6.879 81.765 1122 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.57 % Allowed : 30.26 % Favored : 66.17 % 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: -0.80 (0.26), residues: 1002 helix: 0.92 (0.28), residues: 394 sheet: -0.16 (0.37), residues: 179 loop : -2.14 (0.26), residues: 429 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 E 107 TYR 0.009 0.001 TYR E 128 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 322) hydrogen bonds : angle 3.86209 ( 936) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.29722 ( 6) covalent geometry : bond 0.00248 ( 8096) covalent geometry : angle 0.53509 (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 138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 70 TYR cc_start: 0.8384 (t80) cc_final: 0.8082 (t80) REVERT: B 17 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 57 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8583 (mttt) REVERT: B 163 ASP cc_start: 0.7119 (t0) cc_final: 0.6875 (t0) REVERT: B 314 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8141 (mtt180) REVERT: C 273 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8212 (tt) REVERT: G 9 ILE cc_start: 0.4291 (OUTLIER) cc_final: 0.3902 (pp) outliers start: 31 outliers final: 26 residues processed: 133 average time/residue: 0.2283 time to fit residues: 40.0902 Evaluate side-chains 134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 48 THR 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 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE 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 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: 0.6980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.0040 chunk 92 optimal weight: 1.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.151346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099383 restraints weight = 9512.582| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.47 r_work: 0.3063 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8099 Z= 0.145 Angle : 0.560 16.938 10971 Z= 0.291 Chirality : 0.042 0.208 1271 Planarity : 0.004 0.048 1382 Dihedral : 6.885 83.100 1122 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.14 % Allowed : 29.69 % Favored : 66.17 % 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: -0.82 (0.26), residues: 1002 helix: 0.91 (0.28), residues: 394 sheet: -0.24 (0.37), residues: 181 loop : -2.14 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS C 213 PHE 0.013 0.001 PHE B 241 TYR 0.013 0.001 TYR B 111 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 322) hydrogen bonds : angle 3.87322 ( 936) SS BOND : bond 0.00101 ( 3) SS BOND : angle 0.35581 ( 6) covalent geometry : bond 0.00345 ( 8096) covalent geometry : angle 0.56040 (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: 36 poor density : 106 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: E 70 TYR cc_start: 0.8378 (t80) cc_final: 0.8073 (t80) REVERT: B 17 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 57 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8579 (mttt) REVERT: B 163 ASP cc_start: 0.7167 (t0) cc_final: 0.6943 (t0) REVERT: B 314 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8102 (mtt180) REVERT: C 273 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8200 (tt) REVERT: G 9 ILE cc_start: 0.4139 (OUTLIER) cc_final: 0.3764 (pp) REVERT: G 48 ASP cc_start: 0.8782 (t0) cc_final: 0.8481 (t0) outliers start: 36 outliers final: 28 residues processed: 137 average time/residue: 0.2050 time to fit residues: 37.5462 Evaluate side-chains 137 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 ILE 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 19 HIS Chi-restraints excluded: chain F residue 44 LEU 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 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 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: 0.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.153346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101290 restraints weight = 9535.849| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.50 r_work: 0.3074 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1579 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= 0.128 Angle : 0.548 16.593 10971 Z= 0.285 Chirality : 0.042 0.205 1271 Planarity : 0.003 0.048 1382 Dihedral : 6.681 83.005 1120 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.37 % Allowed : 29.34 % 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: -0.78 (0.26), residues: 1002 helix: 0.96 (0.28), residues: 394 sheet: -0.31 (0.36), residues: 187 loop : -2.10 (0.27), residues: 421 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 0.010 0.001 TYR C 287 ARG 0.006 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 322) hydrogen bonds : angle 3.83300 ( 936) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.30648 ( 6) covalent geometry : bond 0.00300 ( 8096) covalent geometry : angle 0.54814 (10965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5089.89 seconds wall clock time: 87 minutes 41.11 seconds (5261.11 seconds total)