Starting phenix.real_space_refine on Sat Aug 23 02:37:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jis_36326/08_2025/8jis_36326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jis_36326/08_2025/8jis_36326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jis_36326/08_2025/8jis_36326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jis_36326/08_2025/8jis_36326.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jis_36326/08_2025/8jis_36326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jis_36326/08_2025/8jis_36326.map" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5828 2.51 5 N 1574 2.21 5 O 1699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9158 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1856 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2572 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 427 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3104 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 1.81, per 1000 atoms: 0.20 Number of scatterers: 9158 At special positions: 0 Unit cell: (86.751, 95.319, 173.502, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1699 8.00 N 1574 7.00 C 5828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 334.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 40.5% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.643A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.723A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.648A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.796A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 4.051A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.074A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.655A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'R' and resid 31 through 49 Processing helix chain 'R' and resid 89 through 93 Processing helix chain 'R' and resid 139 through 169 Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.683A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 211 Processing helix chain 'R' and resid 216 through 221 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.584A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 292 Proline residue: R 277 - end of helix removed outlier: 3.963A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.830A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.587A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 354 removed outlier: 4.145A pdb=" N CYS R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 361 Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 377 through 404 removed outlier: 3.762A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 removed outlier: 3.814A pdb=" N GLU R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.630A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.502A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.763A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.742A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.978A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.734A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.980A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.516A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 112 through 114 removed outlier: 4.646A pdb=" N ASP R 114 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU R 118 " --> pdb=" O ASP R 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 443 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1496 1.31 - 1.44: 2689 1.44 - 1.56: 5100 1.56 - 1.69: 1 1.69 - 1.82: 78 Bond restraints: 9364 Sorted by residual: bond pdb=" C ASP R 53 " pdb=" N PRO R 54 " ideal model delta sigma weight residual 1.331 1.385 -0.054 8.70e-03 1.32e+04 3.87e+01 bond pdb=" C GLU A 311 " pdb=" O GLU A 311 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.26e-02 6.30e+03 2.01e+01 bond pdb=" CA ALA R 368 " pdb=" C ALA R 368 " ideal model delta sigma weight residual 1.523 1.487 0.036 8.20e-03 1.49e+04 1.97e+01 bond pdb=" CA ALA B 328 " pdb=" C ALA B 328 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.18e-02 7.18e+03 1.90e+01 bond pdb=" CA SER B 191 " pdb=" C SER B 191 " ideal model delta sigma weight residual 1.520 1.472 0.048 1.12e-02 7.97e+03 1.83e+01 ... (remaining 9359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 12304 2.97 - 5.93: 343 5.93 - 8.90: 65 8.90 - 11.86: 10 11.86 - 14.83: 2 Bond angle restraints: 12724 Sorted by residual: angle pdb=" N HIS R 374 " pdb=" CA HIS R 374 " pdb=" C HIS R 374 " ideal model delta sigma weight residual 114.12 99.29 14.83 1.39e+00 5.18e-01 1.14e+02 angle pdb=" N ASP R 344 " pdb=" CA ASP R 344 " pdb=" C ASP R 344 " ideal model delta sigma weight residual 113.19 101.25 11.94 1.19e+00 7.06e-01 1.01e+02 angle pdb=" N GLU A 281 " pdb=" CA GLU A 281 " pdb=" C GLU A 281 " ideal model delta sigma weight residual 112.34 101.39 10.95 1.30e+00 5.92e-01 7.09e+01 angle pdb=" N ILE R 345 " pdb=" CA ILE R 345 " pdb=" C ILE R 345 " ideal model delta sigma weight residual 110.42 102.95 7.47 9.60e-01 1.09e+00 6.06e+01 angle pdb=" N SER R 93 " pdb=" CA SER R 93 " pdb=" C SER R 93 " ideal model delta sigma weight residual 112.23 103.05 9.18 1.26e+00 6.30e-01 5.31e+01 ... (remaining 12719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4676 17.50 - 35.01: 523 35.01 - 52.51: 231 52.51 - 70.02: 75 70.02 - 87.52: 20 Dihedral angle restraints: 5525 sinusoidal: 2097 harmonic: 3428 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 -179.90 -87.10 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -127.73 41.73 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA CYS R 46 " pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " ideal model delta sinusoidal sigma weight residual -73.00 -6.57 -66.43 1 2.00e+01 2.50e-03 1.44e+01 ... (remaining 5522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1140 0.081 - 0.161: 214 0.161 - 0.242: 52 0.242 - 0.322: 18 0.322 - 0.402: 7 Chirality restraints: 1431 Sorted by residual: chirality pdb=" CA THR N 111 " pdb=" N THR N 111 " pdb=" C THR N 111 " pdb=" CB THR N 111 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA SER B 136 " pdb=" N SER B 136 " pdb=" C SER B 136 " pdb=" CB SER B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 1428 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO R 90 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C PRO R 90 " 0.067 2.00e-02 2.50e+03 pdb=" O PRO R 90 " -0.024 2.00e-02 2.50e+03 pdb=" N TRP R 91 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 280 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C PRO A 280 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO A 280 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 281 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 42 " 0.014 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C GLU G 42 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU G 42 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA G 43 " 0.018 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2581 2.79 - 3.32: 8268 3.32 - 3.85: 15774 3.85 - 4.37: 18580 4.37 - 4.90: 30732 Nonbonded interactions: 75935 Sorted by model distance: nonbonded pdb=" OD2 ASP A 26 " pdb=" NZ LYS B 78 " model vdw 2.266 3.120 nonbonded pdb=" O SER A 44 " pdb=" OG SER A 44 " model vdw 2.294 3.040 nonbonded pdb=" O LEU R 349 " pdb=" OG1 THR R 353 " model vdw 2.303 3.040 nonbonded pdb=" N HIS R 374 " pdb=" N ALA R 375 " model vdw 2.320 2.560 nonbonded pdb=" OE2 GLU A 20 " pdb=" NZ LYS B 89 " model vdw 2.346 3.120 ... (remaining 75930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.009 0.057 9369 Z= 0.659 Angle : 1.200 14.827 12734 Z= 0.787 Chirality : 0.077 0.402 1431 Planarity : 0.005 0.067 1619 Dihedral : 19.441 87.521 3292 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.91 % Favored : 92.23 % Rotamer: Outliers : 14.75 % Allowed : 17.86 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.24), residues: 1158 helix: 0.00 (0.25), residues: 418 sheet: -0.37 (0.33), residues: 215 loop : -1.64 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 62 TYR 0.027 0.002 TYR R 148 PHE 0.024 0.002 PHE B 199 TRP 0.025 0.002 TRP A 211 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00921 ( 9364) covalent geometry : angle 1.19965 (12724) SS BOND : bond 0.00619 ( 5) SS BOND : angle 1.57858 ( 10) hydrogen bonds : bond 0.22854 ( 443) hydrogen bonds : angle 7.47247 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 171 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8569 (m) REVERT: A 324 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.8622 (p-80) REVERT: A 359 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: B 175 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7625 (mp10) REVERT: B 186 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: B 228 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: B 292 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8551 (m-10) REVERT: P 21 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8520 (tm-30) REVERT: G 21 MET cc_start: 0.6642 (ppp) cc_final: 0.6419 (ppp) REVERT: G 46 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8699 (tppt) REVERT: G 50 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7350 (mm) REVERT: N 34 MET cc_start: 0.8307 (mmm) cc_final: 0.8043 (mmm) REVERT: N 46 GLU cc_start: 0.8158 (pt0) cc_final: 0.7764 (mm-30) REVERT: N 53 GLN cc_start: 0.8153 (mp10) cc_final: 0.7910 (mp10) REVERT: R 31 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8208 (p) REVERT: R 42 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: R 107 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.4981 (pm20) REVERT: R 261 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.6972 (t) REVERT: R 346 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5609 (mmtt) REVERT: R 351 LYS cc_start: 0.8762 (tmtp) cc_final: 0.8389 (tptp) REVERT: R 369 PHE cc_start: 0.8034 (m-80) cc_final: 0.7719 (m-80) outliers start: 142 outliers final: 20 residues processed: 272 average time/residue: 0.4707 time to fit residues: 136.0845 Evaluate side-chains 172 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 190 GLN B 230 ASN G 44 HIS R 63 ASN R 180 HIS R 406 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.129985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085871 restraints weight = 15306.912| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.08 r_work: 0.3043 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9369 Z= 0.156 Angle : 0.650 11.306 12734 Z= 0.346 Chirality : 0.042 0.184 1431 Planarity : 0.005 0.061 1619 Dihedral : 8.554 84.681 1332 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.42 % Rotamer: Outliers : 5.92 % Allowed : 23.88 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.25), residues: 1158 helix: 1.33 (0.25), residues: 442 sheet: 0.15 (0.34), residues: 211 loop : -1.44 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 214 TYR 0.025 0.001 TYR R 148 PHE 0.018 0.002 PHE A 307 TRP 0.015 0.002 TRP R 110 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9364) covalent geometry : angle 0.64913 (12724) SS BOND : bond 0.00263 ( 5) SS BOND : angle 1.49309 ( 10) hydrogen bonds : bond 0.05228 ( 443) hydrogen bonds : angle 4.88557 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8688 (mt0) cc_final: 0.8399 (mt0) REVERT: A 209 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8689 (ptp-170) REVERT: B 59 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: B 175 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7852 (mp10) REVERT: B 186 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: B 217 MET cc_start: 0.8973 (pmt) cc_final: 0.8572 (pmm) REVERT: P 15 ASP cc_start: 0.8362 (t70) cc_final: 0.8148 (t0) REVERT: P 21 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8565 (tm-30) REVERT: G 21 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6294 (ppp) REVERT: G 46 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8579 (tppt) REVERT: G 50 LEU cc_start: 0.7805 (mm) cc_final: 0.7561 (mm) REVERT: N 46 GLU cc_start: 0.8260 (pt0) cc_final: 0.7991 (mm-30) REVERT: N 53 GLN cc_start: 0.8241 (mp10) cc_final: 0.7876 (mp10) REVERT: N 122 THR cc_start: 0.7421 (m) cc_final: 0.7013 (p) REVERT: R 42 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: R 107 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: R 112 GLN cc_start: 0.7554 (mm110) cc_final: 0.7191 (mm110) REVERT: R 261 SER cc_start: 0.6834 (OUTLIER) cc_final: 0.6560 (t) REVERT: R 346 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.5237 (mmtt) REVERT: R 370 VAL cc_start: 0.5237 (OUTLIER) cc_final: 0.4895 (t) REVERT: R 371 MET cc_start: 0.8609 (mpp) cc_final: 0.8105 (mpp) outliers start: 57 outliers final: 15 residues processed: 208 average time/residue: 0.4805 time to fit residues: 106.2371 Evaluate side-chains 170 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 357 GLN B 230 ASN R 37 GLN R 180 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.126493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.082034 restraints weight = 15440.267| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.07 r_work: 0.2950 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9369 Z= 0.177 Angle : 0.603 8.314 12734 Z= 0.322 Chirality : 0.042 0.161 1431 Planarity : 0.004 0.052 1619 Dihedral : 7.038 81.951 1304 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.09 % Allowed : 25.96 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.25), residues: 1158 helix: 1.77 (0.25), residues: 440 sheet: 0.25 (0.34), residues: 225 loop : -1.22 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 43 TYR 0.026 0.001 TYR R 148 PHE 0.015 0.001 PHE A 307 TRP 0.011 0.001 TRP R 243 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9364) covalent geometry : angle 0.60274 (12724) SS BOND : bond 0.00251 ( 5) SS BOND : angle 1.09475 ( 10) hydrogen bonds : bond 0.04621 ( 443) hydrogen bonds : angle 4.55127 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 37 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.6529 (pp) REVERT: B 59 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: B 175 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7990 (mp10) REVERT: B 217 MET cc_start: 0.9071 (pmt) cc_final: 0.8627 (pmm) REVERT: B 220 GLN cc_start: 0.8458 (mp10) cc_final: 0.8220 (mp10) REVERT: B 336 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8849 (mt) REVERT: P 16 GLU cc_start: 0.8589 (tp30) cc_final: 0.8214 (mm-30) REVERT: P 17 GLN cc_start: 0.8550 (tt0) cc_final: 0.8286 (tp40) REVERT: P 21 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8548 (tm-30) REVERT: G 38 MET cc_start: 0.7679 (mtp) cc_final: 0.7443 (mtm) REVERT: N 46 GLU cc_start: 0.8357 (pt0) cc_final: 0.8024 (mm-30) REVERT: N 53 GLN cc_start: 0.8370 (mp10) cc_final: 0.7821 (mp10) REVERT: N 65 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8935 (ttpp) REVERT: N 122 THR cc_start: 0.7316 (m) cc_final: 0.6938 (p) REVERT: R 42 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: R 112 GLN cc_start: 0.7833 (mm110) cc_final: 0.7447 (mm110) REVERT: R 221 GLN cc_start: 0.8043 (mm110) cc_final: 0.7749 (mm110) REVERT: R 371 MET cc_start: 0.8637 (mpp) cc_final: 0.8173 (mpp) outliers start: 49 outliers final: 19 residues processed: 187 average time/residue: 0.4780 time to fit residues: 95.1555 Evaluate side-chains 157 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 213 GLN Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 109 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.128012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083957 restraints weight = 15597.300| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.11 r_work: 0.2968 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9369 Z= 0.117 Angle : 0.557 8.484 12734 Z= 0.296 Chirality : 0.040 0.150 1431 Planarity : 0.004 0.051 1619 Dihedral : 5.676 81.606 1284 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 4.47 % Allowed : 26.06 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1158 helix: 2.20 (0.25), residues: 435 sheet: 0.36 (0.35), residues: 227 loop : -1.14 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 62 TYR 0.022 0.001 TYR R 148 PHE 0.015 0.001 PHE A 189 TRP 0.018 0.001 TRP R 39 HIS 0.001 0.000 HIS R 374 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9364) covalent geometry : angle 0.55640 (12724) SS BOND : bond 0.00247 ( 5) SS BOND : angle 1.09312 ( 10) hydrogen bonds : bond 0.03952 ( 443) hydrogen bonds : angle 4.27217 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8280 (mm-30) REVERT: A 239 ASP cc_start: 0.8688 (m-30) cc_final: 0.8481 (t0) REVERT: B 37 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.6529 (pt) REVERT: B 59 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: B 127 LYS cc_start: 0.8712 (mptt) cc_final: 0.8502 (tppp) REVERT: B 175 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7981 (mp10) REVERT: B 217 MET cc_start: 0.9103 (pmt) cc_final: 0.8635 (pmm) REVERT: B 280 LYS cc_start: 0.8878 (tppp) cc_final: 0.7871 (tptp) REVERT: B 336 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8796 (mp) REVERT: P 16 GLU cc_start: 0.8570 (tp30) cc_final: 0.8157 (mm-30) REVERT: P 17 GLN cc_start: 0.8500 (tt0) cc_final: 0.8250 (tp40) REVERT: P 21 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8430 (tm-30) REVERT: G 38 MET cc_start: 0.7730 (mtp) cc_final: 0.7516 (mtm) REVERT: G 46 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8655 (tppt) REVERT: N 46 GLU cc_start: 0.8283 (pt0) cc_final: 0.7950 (mm-30) REVERT: N 53 GLN cc_start: 0.8406 (mp10) cc_final: 0.7847 (mp10) REVERT: N 122 THR cc_start: 0.7071 (m) cc_final: 0.6757 (p) REVERT: R 42 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: R 112 GLN cc_start: 0.7781 (mm110) cc_final: 0.7555 (mm110) REVERT: R 371 MET cc_start: 0.8582 (mpp) cc_final: 0.7897 (mpp) outliers start: 43 outliers final: 19 residues processed: 190 average time/residue: 0.4334 time to fit residues: 87.7105 Evaluate side-chains 162 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 84 optimal weight: 40.0000 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.127361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083293 restraints weight = 15602.111| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.10 r_work: 0.2959 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9369 Z= 0.128 Angle : 0.548 7.215 12734 Z= 0.293 Chirality : 0.040 0.148 1431 Planarity : 0.004 0.052 1619 Dihedral : 5.578 80.826 1283 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 4.05 % Allowed : 26.38 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.26), residues: 1158 helix: 2.43 (0.25), residues: 429 sheet: 0.45 (0.35), residues: 227 loop : -1.14 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 67 TYR 0.022 0.001 TYR R 148 PHE 0.014 0.001 PHE A 189 TRP 0.011 0.001 TRP A 211 HIS 0.001 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9364) covalent geometry : angle 0.54756 (12724) SS BOND : bond 0.00219 ( 5) SS BOND : angle 1.10994 ( 10) hydrogen bonds : bond 0.03883 ( 443) hydrogen bonds : angle 4.20214 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 239 ASP cc_start: 0.8669 (m-30) cc_final: 0.8466 (t0) REVERT: B 37 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.6610 (pt) REVERT: B 59 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: B 127 LYS cc_start: 0.8703 (mptt) cc_final: 0.8472 (tppp) REVERT: B 175 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7989 (mp10) REVERT: B 186 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: B 217 MET cc_start: 0.9132 (pmt) cc_final: 0.8681 (pmm) REVERT: B 280 LYS cc_start: 0.8890 (tppp) cc_final: 0.7880 (tptp) REVERT: B 336 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8770 (mp) REVERT: P 16 GLU cc_start: 0.8621 (tp30) cc_final: 0.8166 (mm-30) REVERT: P 17 GLN cc_start: 0.8503 (tt0) cc_final: 0.8282 (tp40) REVERT: P 21 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8434 (tm-30) REVERT: N 46 GLU cc_start: 0.8327 (pt0) cc_final: 0.7983 (mm-30) REVERT: N 53 GLN cc_start: 0.8361 (mp10) cc_final: 0.7672 (mp10) REVERT: N 87 LYS cc_start: 0.8194 (ptpp) cc_final: 0.7846 (ptpp) REVERT: N 122 THR cc_start: 0.7096 (m) cc_final: 0.6771 (p) REVERT: R 42 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: R 112 GLN cc_start: 0.7513 (mm110) cc_final: 0.7234 (mm110) REVERT: R 371 MET cc_start: 0.8644 (mpp) cc_final: 0.7936 (mpp) outliers start: 39 outliers final: 26 residues processed: 183 average time/residue: 0.6510 time to fit residues: 126.6379 Evaluate side-chains 170 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 216 ASN N 3 GLN R 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.127073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.083106 restraints weight = 15508.650| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.10 r_work: 0.2955 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9369 Z= 0.131 Angle : 0.555 9.364 12734 Z= 0.295 Chirality : 0.040 0.152 1431 Planarity : 0.004 0.053 1619 Dihedral : 5.524 79.852 1283 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 4.98 % Allowed : 26.06 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1158 helix: 2.38 (0.25), residues: 434 sheet: 0.54 (0.35), residues: 227 loop : -1.03 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 250 TYR 0.021 0.001 TYR R 148 PHE 0.014 0.001 PHE A 189 TRP 0.011 0.001 TRP A 211 HIS 0.001 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9364) covalent geometry : angle 0.55473 (12724) SS BOND : bond 0.00204 ( 5) SS BOND : angle 1.08930 ( 10) hydrogen bonds : bond 0.03835 ( 443) hydrogen bonds : angle 4.15412 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8216 (mm-30) REVERT: A 239 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8461 (t0) REVERT: B 37 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.6635 (pt) REVERT: B 59 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: B 127 LYS cc_start: 0.8689 (mptt) cc_final: 0.8450 (tppp) REVERT: B 175 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7886 (mp10) REVERT: B 186 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: B 217 MET cc_start: 0.9119 (pmt) cc_final: 0.8712 (pmm) REVERT: B 228 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: B 280 LYS cc_start: 0.8897 (tppp) cc_final: 0.7880 (tptp) REVERT: B 336 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8777 (mp) REVERT: P 16 GLU cc_start: 0.8635 (tp30) cc_final: 0.8163 (mm-30) REVERT: P 17 GLN cc_start: 0.8493 (tt0) cc_final: 0.8293 (tp40) REVERT: P 21 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8487 (tm-30) REVERT: G 21 MET cc_start: 0.6756 (tmm) cc_final: 0.6490 (ttm) REVERT: N 46 GLU cc_start: 0.8331 (pt0) cc_final: 0.7986 (mm-30) REVERT: N 53 GLN cc_start: 0.8448 (mp10) cc_final: 0.7715 (mp10) REVERT: N 87 LYS cc_start: 0.8303 (ptpp) cc_final: 0.8090 (ptpp) REVERT: N 122 THR cc_start: 0.7095 (m) cc_final: 0.6775 (p) REVERT: R 42 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: R 45 GLN cc_start: 0.7867 (pt0) cc_final: 0.7436 (pp30) REVERT: R 112 GLN cc_start: 0.7525 (mm110) cc_final: 0.7207 (mm110) outliers start: 48 outliers final: 28 residues processed: 184 average time/residue: 0.5970 time to fit residues: 117.3460 Evaluate side-chains 170 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL 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 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN N 3 GLN R 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.125561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081190 restraints weight = 15569.595| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.10 r_work: 0.2921 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9369 Z= 0.195 Angle : 0.611 9.320 12734 Z= 0.325 Chirality : 0.043 0.312 1431 Planarity : 0.004 0.055 1619 Dihedral : 5.722 80.022 1283 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.98 % Allowed : 26.38 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.25), residues: 1158 helix: 2.34 (0.24), residues: 431 sheet: 0.56 (0.34), residues: 225 loop : -1.03 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 250 TYR 0.024 0.002 TYR R 148 PHE 0.015 0.001 PHE N 108 TRP 0.012 0.001 TRP A 211 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 9364) covalent geometry : angle 0.60864 (12724) SS BOND : bond 0.00566 ( 5) SS BOND : angle 1.82682 ( 10) hydrogen bonds : bond 0.04199 ( 443) hydrogen bonds : angle 4.26237 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8193 (mm-30) REVERT: B 37 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.6723 (pt) REVERT: B 59 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: B 127 LYS cc_start: 0.8718 (mptt) cc_final: 0.8476 (tppp) REVERT: B 175 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7864 (mp10) REVERT: B 186 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: B 217 MET cc_start: 0.9130 (pmt) cc_final: 0.8688 (pmm) REVERT: B 220 GLN cc_start: 0.8318 (mp10) cc_final: 0.8117 (mp10) REVERT: B 336 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8816 (mp) REVERT: P 16 GLU cc_start: 0.8641 (tp30) cc_final: 0.8411 (tp30) REVERT: P 17 GLN cc_start: 0.8433 (tt0) cc_final: 0.8221 (tp40) REVERT: P 21 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8502 (tm-30) REVERT: G 21 MET cc_start: 0.6839 (tmm) cc_final: 0.6599 (ttm) REVERT: N 46 GLU cc_start: 0.8371 (pt0) cc_final: 0.8013 (mm-30) REVERT: N 53 GLN cc_start: 0.8402 (mp10) cc_final: 0.7849 (mp10) REVERT: N 87 LYS cc_start: 0.8246 (ptpp) cc_final: 0.7855 (ptpp) REVERT: N 120 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8549 (mm-40) REVERT: N 122 THR cc_start: 0.7222 (m) cc_final: 0.6852 (p) REVERT: R 112 GLN cc_start: 0.7369 (mm110) cc_final: 0.7116 (mm110) REVERT: R 204 MET cc_start: 0.6825 (mmm) cc_final: 0.6544 (mmm) REVERT: R 371 MET cc_start: 0.8683 (mpp) cc_final: 0.8016 (mpp) outliers start: 48 outliers final: 29 residues processed: 180 average time/residue: 0.6017 time to fit residues: 115.4625 Evaluate side-chains 170 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 422 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN R 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.126651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082377 restraints weight = 15508.020| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.10 r_work: 0.2940 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9369 Z= 0.141 Angle : 0.596 10.567 12734 Z= 0.318 Chirality : 0.041 0.228 1431 Planarity : 0.004 0.054 1619 Dihedral : 5.463 79.581 1281 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.95 % Allowed : 27.73 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.25), residues: 1158 helix: 2.40 (0.25), residues: 431 sheet: 0.57 (0.35), residues: 225 loop : -1.01 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 250 TYR 0.021 0.001 TYR R 148 PHE 0.014 0.001 PHE A 189 TRP 0.011 0.001 TRP A 211 HIS 0.001 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9364) covalent geometry : angle 0.59488 (12724) SS BOND : bond 0.00201 ( 5) SS BOND : angle 1.65092 ( 10) hydrogen bonds : bond 0.03964 ( 443) hydrogen bonds : angle 4.20677 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8206 (mm-30) REVERT: B 37 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.6745 (pp) REVERT: B 59 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: B 127 LYS cc_start: 0.8733 (mptt) cc_final: 0.8483 (tppp) REVERT: B 175 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7846 (mp10) REVERT: B 186 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: B 217 MET cc_start: 0.9129 (pmt) cc_final: 0.8706 (pmm) REVERT: B 228 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8341 (m-30) REVERT: B 280 LYS cc_start: 0.8906 (tppp) cc_final: 0.8444 (tptp) REVERT: B 336 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8794 (mt) REVERT: P 16 GLU cc_start: 0.8639 (tp30) cc_final: 0.8415 (tp30) REVERT: P 17 GLN cc_start: 0.8444 (tt0) cc_final: 0.8238 (tp40) REVERT: P 21 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8494 (tm-30) REVERT: G 21 MET cc_start: 0.6827 (tmm) cc_final: 0.6601 (ttm) REVERT: N 46 GLU cc_start: 0.8351 (pt0) cc_final: 0.8000 (mm-30) REVERT: N 53 GLN cc_start: 0.8469 (mp10) cc_final: 0.7863 (mp10) REVERT: N 87 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7936 (ptpp) REVERT: N 120 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8532 (mm-40) REVERT: N 122 THR cc_start: 0.7166 (m) cc_final: 0.6834 (p) REVERT: R 42 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: R 204 MET cc_start: 0.6741 (mmm) cc_final: 0.6468 (mmm) outliers start: 38 outliers final: 26 residues processed: 174 average time/residue: 0.6310 time to fit residues: 117.1309 Evaluate side-chains 168 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL 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 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 230 ASN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.082988 restraints weight = 15533.832| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.11 r_work: 0.2970 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9369 Z= 0.132 Angle : 0.603 11.092 12734 Z= 0.318 Chirality : 0.041 0.200 1431 Planarity : 0.004 0.053 1619 Dihedral : 5.376 77.736 1281 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 3.84 % Allowed : 28.04 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.25), residues: 1158 helix: 2.52 (0.24), residues: 428 sheet: 0.61 (0.35), residues: 225 loop : -1.01 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 62 TYR 0.020 0.001 TYR R 148 PHE 0.013 0.001 PHE A 189 TRP 0.011 0.001 TRP A 211 HIS 0.002 0.000 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9364) covalent geometry : angle 0.60249 (12724) SS BOND : bond 0.00259 ( 5) SS BOND : angle 1.36700 ( 10) hydrogen bonds : bond 0.03840 ( 443) hydrogen bonds : angle 4.15429 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8207 (mm-30) REVERT: B 37 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.6753 (pp) REVERT: B 59 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: B 127 LYS cc_start: 0.8718 (mptt) cc_final: 0.8449 (tppp) REVERT: B 186 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: B 217 MET cc_start: 0.9171 (pmt) cc_final: 0.8775 (pmm) REVERT: B 228 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8321 (m-30) REVERT: B 280 LYS cc_start: 0.8906 (tppp) cc_final: 0.8457 (tptp) REVERT: B 336 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8788 (mp) REVERT: P 16 GLU cc_start: 0.8669 (tp30) cc_final: 0.8189 (mm-30) REVERT: P 17 GLN cc_start: 0.8453 (tt0) cc_final: 0.8252 (tp40) REVERT: P 21 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8496 (tm-30) REVERT: G 21 MET cc_start: 0.6751 (tmm) cc_final: 0.6536 (ttm) REVERT: N 46 GLU cc_start: 0.8354 (pt0) cc_final: 0.7997 (mm-30) REVERT: N 53 GLN cc_start: 0.8485 (mp10) cc_final: 0.7788 (mp10) REVERT: N 87 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7886 (ptpp) REVERT: N 120 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8545 (mm-40) REVERT: N 122 THR cc_start: 0.7158 (m) cc_final: 0.6846 (p) REVERT: R 42 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: R 112 GLN cc_start: 0.7714 (mm110) cc_final: 0.7428 (mm110) REVERT: R 204 MET cc_start: 0.6733 (mmm) cc_final: 0.6449 (mmm) REVERT: R 415 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7485 (ptpt) outliers start: 37 outliers final: 26 residues processed: 170 average time/residue: 0.6004 time to fit residues: 108.5873 Evaluate side-chains 172 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL 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 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 15 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 175 GLN B 230 ASN R 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.126897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082628 restraints weight = 15508.344| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.11 r_work: 0.2966 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9369 Z= 0.141 Angle : 0.619 14.373 12734 Z= 0.324 Chirality : 0.041 0.181 1431 Planarity : 0.004 0.053 1619 Dihedral : 5.312 76.515 1281 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 3.43 % Allowed : 28.35 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.25), residues: 1158 helix: 2.56 (0.24), residues: 428 sheet: 0.58 (0.34), residues: 225 loop : -0.97 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 62 TYR 0.021 0.001 TYR R 148 PHE 0.013 0.001 PHE A 189 TRP 0.011 0.001 TRP A 211 HIS 0.001 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9364) covalent geometry : angle 0.61835 (12724) SS BOND : bond 0.00230 ( 5) SS BOND : angle 1.21567 ( 10) hydrogen bonds : bond 0.03861 ( 443) hydrogen bonds : angle 4.14252 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 37 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.6795 (pp) REVERT: B 59 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: B 186 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: B 217 MET cc_start: 0.9174 (pmt) cc_final: 0.8725 (pmm) REVERT: B 226 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 228 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: B 280 LYS cc_start: 0.8905 (tppp) cc_final: 0.8444 (tptp) REVERT: B 336 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8789 (mp) REVERT: P 16 GLU cc_start: 0.8687 (tp30) cc_final: 0.8462 (tp30) REVERT: P 21 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8511 (tm-30) REVERT: G 21 MET cc_start: 0.6847 (tmm) cc_final: 0.6636 (ttm) REVERT: N 46 GLU cc_start: 0.8372 (pt0) cc_final: 0.8007 (mm-30) REVERT: N 53 GLN cc_start: 0.8484 (mp10) cc_final: 0.7831 (mp10) REVERT: N 87 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7933 (ptpp) REVERT: N 122 THR cc_start: 0.7179 (m) cc_final: 0.6834 (p) REVERT: R 42 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: R 112 GLN cc_start: 0.7636 (mm110) cc_final: 0.6838 (mp10) REVERT: R 204 MET cc_start: 0.6767 (mmm) cc_final: 0.6492 (mmm) REVERT: R 371 MET cc_start: 0.8513 (mpp) cc_final: 0.8286 (mmt) REVERT: R 415 LYS cc_start: 0.7743 (mtmt) cc_final: 0.7472 (ptpt) outliers start: 33 outliers final: 23 residues processed: 171 average time/residue: 0.6405 time to fit residues: 116.7749 Evaluate side-chains 172 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL 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 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 246 ASN B 175 GLN B 230 ASN R 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.126374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082057 restraints weight = 15318.183| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.09 r_work: 0.2935 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9369 Z= 0.159 Angle : 0.634 16.309 12734 Z= 0.330 Chirality : 0.041 0.182 1431 Planarity : 0.004 0.054 1619 Dihedral : 4.752 49.876 1278 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 4.15 % Allowed : 27.62 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.26), residues: 1158 helix: 2.54 (0.24), residues: 428 sheet: 0.53 (0.34), residues: 231 loop : -0.95 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 62 TYR 0.022 0.001 TYR R 148 PHE 0.018 0.001 PHE A 189 TRP 0.011 0.001 TRP A 211 HIS 0.001 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9364) covalent geometry : angle 0.63337 (12724) SS BOND : bond 0.00228 ( 5) SS BOND : angle 1.20157 ( 10) hydrogen bonds : bond 0.04002 ( 443) hydrogen bonds : angle 4.17870 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4487.32 seconds wall clock time: 77 minutes 3.99 seconds (4623.99 seconds total)