Starting phenix.real_space_refine on Wed Sep 17 15:08:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivg_60927/09_2025/9ivg_60927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivg_60927/09_2025/9ivg_60927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivg_60927/09_2025/9ivg_60927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivg_60927/09_2025/9ivg_60927.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivg_60927/09_2025/9ivg_60927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivg_60927/09_2025/9ivg_60927.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 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 56 5.16 5 C 5930 2.51 5 N 1612 2.21 5 O 1727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9325 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 160 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "R" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3161 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2014 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "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} Time building chain proxies: 2.50, per 1000 atoms: 0.27 Number of scatterers: 9325 At special positions: 0 Unit cell: (80.325, 99.603, 169.218, 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 56 16.00 O 1727 8.00 N 1612 7.00 C 5930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 349.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 41.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'P' and resid 9 through 29 removed outlier: 4.717A pdb=" N THR P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 53 Processing helix chain 'R' and resid 89 through 93 removed outlier: 3.552A pdb=" N ALA R 92 " --> pdb=" O LEU R 89 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 89 through 93' Processing helix chain 'R' and resid 112 through 116 Processing helix chain 'R' and resid 141 through 169 Processing helix chain 'R' and resid 170 through 173 removed outlier: 3.869A pdb=" N HIS R 173 " --> pdb=" O ARG R 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 170 through 173' Processing helix chain 'R' and resid 174 through 210 removed outlier: 3.798A pdb=" N GLN R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 220 Processing helix chain 'R' and resid 227 through 256 removed outlier: 3.596A pdb=" N LEU R 245 " --> pdb=" O TYR R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Processing helix chain 'R' and resid 275 through 288 removed outlier: 3.547A pdb=" N LEU R 279 " --> pdb=" O GLY R 275 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 305 No H-bonds generated for 'chain 'R' and resid 303 through 305' Processing helix chain 'R' and resid 306 through 336 Proline residue: R 312 - end of helix removed outlier: 3.620A pdb=" N ASN R 320 " --> pdb=" O ALA R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 361 removed outlier: 4.128A pdb=" N LEU R 349 " --> pdb=" O ILE R 345 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 Processing helix chain 'R' and resid 377 through 404 removed outlier: 3.710A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU R 388 " --> pdb=" O LEU R 384 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 removed outlier: 3.803A pdb=" N LEU R 422 " --> pdb=" O GLU R 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.681A pdb=" N VAL A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.523A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.551A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.508A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.692A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.575A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 79 through 84 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 212 removed outlier: 6.122A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 364 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.370A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.634A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.869A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.804A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.692A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.525A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.735A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.530A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1293 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: 1.52 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3041 1.34 - 1.46: 2300 1.46 - 1.58: 4118 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9535 Sorted by residual: bond pdb=" N ASP A 323 " pdb=" CA ASP A 323 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.42e-02 4.96e+03 5.15e+00 bond pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 1.473 1.441 0.032 1.40e-02 5.10e+03 5.08e+00 bond pdb=" N PRO A 326 " pdb=" CD PRO A 326 " ideal model delta sigma weight residual 1.473 1.444 0.029 1.40e-02 5.10e+03 4.39e+00 bond pdb=" N GLU A 322 " pdb=" CA GLU A 322 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.25e-02 6.40e+03 4.31e+00 bond pdb=" CA THR A 320 " pdb=" C THR A 320 " ideal model delta sigma weight residual 1.528 1.505 0.023 1.13e-02 7.83e+03 4.21e+00 ... (remaining 9530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 12692 1.68 - 3.37: 194 3.37 - 5.05: 32 5.05 - 6.73: 5 6.73 - 8.42: 5 Bond angle restraints: 12928 Sorted by residual: angle pdb=" N VAL A 217 " pdb=" CA VAL A 217 " pdb=" C VAL A 217 " ideal model delta sigma weight residual 113.53 109.93 3.60 9.80e-01 1.04e+00 1.35e+01 angle pdb=" N PRO A 326 " pdb=" CD PRO A 326 " pdb=" CG PRO A 326 " ideal model delta sigma weight residual 103.20 97.72 5.48 1.50e+00 4.44e-01 1.34e+01 angle pdb=" CA THR A 319 " pdb=" CB THR A 319 " pdb=" OG1 THR A 319 " ideal model delta sigma weight residual 109.60 104.64 4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" CA THR A 320 " pdb=" CB THR A 320 " pdb=" OG1 THR A 320 " ideal model delta sigma weight residual 109.60 104.68 4.92 1.50e+00 4.44e-01 1.07e+01 angle pdb=" CA THR A 325 " pdb=" CB THR A 325 " pdb=" OG1 THR A 325 " ideal model delta sigma weight residual 109.60 104.70 4.90 1.50e+00 4.44e-01 1.07e+01 ... (remaining 12923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4754 17.96 - 35.92: 651 35.92 - 53.88: 195 53.88 - 71.84: 41 71.84 - 89.80: 10 Dihedral angle restraints: 5651 sinusoidal: 2236 harmonic: 3415 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 8.88 84.12 1 1.00e+01 1.00e-02 8.62e+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 -165.10 79.10 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual 93.00 144.63 -51.63 1 1.00e+01 1.00e-02 3.64e+01 ... (remaining 5648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1290 0.067 - 0.134: 136 0.134 - 0.201: 3 0.201 - 0.268: 0 0.268 - 0.335: 1 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CG LEU R 388 " pdb=" CB LEU R 388 " pdb=" CD1 LEU R 388 " pdb=" CD2 LEU R 388 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA TRP R 120 " pdb=" N TRP R 120 " pdb=" C TRP R 120 " pdb=" CB TRP R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CB ILE R 147 " pdb=" CA ILE R 147 " pdb=" CG1 ILE R 147 " pdb=" CG2 ILE R 147 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1427 not shown) Planarity restraints: 1647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 39 " 0.009 2.00e-02 2.50e+03 1.25e-02 3.89e+00 pdb=" CG TRP R 39 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP R 39 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP R 39 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 39 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 39 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 39 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 39 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO B 236 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 327 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO A 328 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 328 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 328 " 0.023 5.00e-02 4.00e+02 ... (remaining 1644 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 225 2.68 - 3.24: 8732 3.24 - 3.79: 14758 3.79 - 4.35: 19579 4.35 - 4.90: 32992 Nonbonded interactions: 76286 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.160 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.239 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.255 3.120 ... (remaining 76281 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.430 Find NCS groups from input model: 0.040 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:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9541 Z= 0.159 Angle : 0.556 8.418 12940 Z= 0.308 Chirality : 0.043 0.335 1430 Planarity : 0.003 0.044 1647 Dihedral : 18.207 89.801 3425 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 3.98 % Allowed : 30.55 % Favored : 65.47 % 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: 0.58 (0.25), residues: 1152 helix: 1.57 (0.26), residues: 440 sheet: 0.42 (0.33), residues: 221 loop : -0.69 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.024 0.001 TYR R 148 PHE 0.012 0.001 PHE B 253 TRP 0.033 0.002 TRP R 39 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9535) covalent geometry : angle 0.55586 (12928) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.96195 ( 12) hydrogen bonds : bond 0.14477 ( 452) hydrogen bonds : angle 6.70021 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8514 (t80) cc_final: 0.8226 (t80) REVERT: R 72 TRP cc_start: 0.4505 (OUTLIER) cc_final: 0.4301 (m-10) REVERT: R 204 MET cc_start: 0.8593 (mmm) cc_final: 0.7879 (mmp) REVERT: R 320 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8589 (t0) REVERT: A 35 GLN cc_start: 0.8775 (tt0) cc_final: 0.8490 (tm-30) REVERT: B 197 ARG cc_start: 0.8726 (tpp80) cc_final: 0.8512 (mmm-85) REVERT: B 268 ASN cc_start: 0.8580 (t0) cc_final: 0.8310 (t0) REVERT: G 18 GLN cc_start: 0.8653 (tp40) cc_final: 0.7939 (tp40) REVERT: G 20 LYS cc_start: 0.9284 (mttt) cc_final: 0.9069 (ttmm) REVERT: N 38 ARG cc_start: 0.9364 (ptt180) cc_final: 0.9086 (ptt90) REVERT: N 73 ASP cc_start: 0.8467 (t0) cc_final: 0.8099 (t0) REVERT: N 82 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8505 (mm-40) REVERT: N 84 ASN cc_start: 0.8497 (m-40) cc_final: 0.8156 (m110) outliers start: 40 outliers final: 15 residues processed: 224 average time/residue: 0.6323 time to fit residues: 150.7963 Evaluate side-chains 178 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 320 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 44 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.112183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.069373 restraints weight = 16709.794| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.88 r_work: 0.2679 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9541 Z= 0.235 Angle : 0.637 7.505 12940 Z= 0.333 Chirality : 0.044 0.184 1430 Planarity : 0.004 0.045 1647 Dihedral : 5.560 52.969 1304 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 5.97 % Allowed : 30.05 % Favored : 63.98 % 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: 0.81 (0.25), residues: 1152 helix: 1.87 (0.25), residues: 455 sheet: 0.53 (0.33), residues: 227 loop : -0.77 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 13 TYR 0.015 0.002 TYR R 148 PHE 0.013 0.001 PHE A 238 TRP 0.013 0.001 TRP R 39 HIS 0.010 0.001 HIS R 99 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 9535) covalent geometry : angle 0.63698 (12928) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.91544 ( 12) hydrogen bonds : bond 0.04462 ( 452) hydrogen bonds : angle 4.69911 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8574 (t80) cc_final: 0.8144 (t80) REVERT: R 204 MET cc_start: 0.8559 (mmm) cc_final: 0.7919 (mmp) REVERT: A 35 GLN cc_start: 0.8720 (tt0) cc_final: 0.8103 (tm-30) REVERT: B 10 GLU cc_start: 0.8874 (tp30) cc_final: 0.8642 (tp30) REVERT: B 197 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8376 (mmm-85) REVERT: B 226 GLU cc_start: 0.8978 (mt-10) cc_final: 0.7926 (mt-10) REVERT: B 260 GLU cc_start: 0.8742 (pt0) cc_final: 0.8278 (tt0) REVERT: B 262 MET cc_start: 0.8642 (mmm) cc_final: 0.8420 (tpp) REVERT: B 268 ASN cc_start: 0.8896 (t0) cc_final: 0.8623 (t0) REVERT: G 18 GLN cc_start: 0.8106 (tp40) cc_final: 0.7477 (tp40) REVERT: G 62 ARG cc_start: 0.5345 (OUTLIER) cc_final: 0.4880 (ptp-170) REVERT: N 6 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8876 (pm20) REVERT: N 38 ARG cc_start: 0.9168 (ptt180) cc_final: 0.8660 (ptt90) REVERT: N 46 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: N 73 ASP cc_start: 0.7824 (t0) cc_final: 0.7515 (t0) REVERT: N 82 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7710 (mm-40) REVERT: N 87 LYS cc_start: 0.7724 (mttm) cc_final: 0.7464 (mtmt) outliers start: 60 outliers final: 25 residues processed: 224 average time/residue: 0.5751 time to fit residues: 137.7597 Evaluate side-chains 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 23 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.070076 restraints weight = 16745.280| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.96 r_work: 0.2712 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9541 Z= 0.131 Angle : 0.592 8.981 12940 Z= 0.304 Chirality : 0.042 0.157 1430 Planarity : 0.004 0.039 1647 Dihedral : 5.003 54.846 1291 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 5.17 % Allowed : 32.74 % Favored : 62.09 % 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: 0.91 (0.25), residues: 1152 helix: 2.09 (0.25), residues: 448 sheet: 0.48 (0.33), residues: 227 loop : -0.78 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.018 0.001 TYR R 145 PHE 0.009 0.001 PHE B 151 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9535) covalent geometry : angle 0.59157 (12928) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.76548 ( 12) hydrogen bonds : bond 0.03908 ( 452) hydrogen bonds : angle 4.40192 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8547 (t80) cc_final: 0.8199 (t80) REVERT: R 204 MET cc_start: 0.8555 (mmm) cc_final: 0.7916 (mmp) REVERT: R 233 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7797 (tpt) REVERT: R 303 MET cc_start: 0.8043 (tmm) cc_final: 0.7817 (tmm) REVERT: A 31 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8173 (tm130) REVERT: A 35 GLN cc_start: 0.8642 (tt0) cc_final: 0.8054 (tm-30) REVERT: A 204 THR cc_start: 0.8932 (p) cc_final: 0.8719 (p) REVERT: A 265 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.9076 (ptm160) REVERT: B 10 GLU cc_start: 0.8874 (tp30) cc_final: 0.8613 (tp30) REVERT: B 197 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8237 (mmm-85) REVERT: B 214 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8571 (ptp-110) REVERT: B 226 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8044 (mt-10) REVERT: B 268 ASN cc_start: 0.8910 (t0) cc_final: 0.8639 (t0) REVERT: G 18 GLN cc_start: 0.8228 (tp40) cc_final: 0.7499 (tp40) REVERT: G 20 LYS cc_start: 0.9114 (ttmm) cc_final: 0.8836 (mttp) REVERT: G 46 LYS cc_start: 0.9508 (mtmm) cc_final: 0.8992 (ptpp) REVERT: G 62 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.5178 (ptp-170) REVERT: N 38 ARG cc_start: 0.9191 (ptt180) cc_final: 0.8738 (ptt90) REVERT: N 46 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: N 73 ASP cc_start: 0.7934 (t0) cc_final: 0.7600 (t0) REVERT: N 82 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7604 (tm-30) REVERT: N 84 ASN cc_start: 0.7816 (m-40) cc_final: 0.7418 (m110) REVERT: N 114 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.8860 (p) outliers start: 52 outliers final: 23 residues processed: 207 average time/residue: 0.5535 time to fit residues: 122.6107 Evaluate side-chains 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 88 ASN N 3 GLN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.070140 restraints weight = 16807.543| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.01 r_work: 0.2716 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9541 Z= 0.126 Angle : 0.587 8.982 12940 Z= 0.299 Chirality : 0.042 0.150 1430 Planarity : 0.003 0.038 1647 Dihedral : 4.517 57.475 1286 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 4.98 % Allowed : 32.94 % Favored : 62.09 % 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: 0.93 (0.26), residues: 1152 helix: 2.10 (0.25), residues: 455 sheet: 0.48 (0.33), residues: 226 loop : -0.79 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.023 0.001 TYR R 69 PHE 0.010 0.001 PHE A 212 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9535) covalent geometry : angle 0.58696 (12928) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.85697 ( 12) hydrogen bonds : bond 0.03669 ( 452) hydrogen bonds : angle 4.23695 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8556 (t80) cc_final: 0.8242 (t80) REVERT: R 80 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6940 (t80) REVERT: R 204 MET cc_start: 0.8554 (mmm) cc_final: 0.7913 (mmp) REVERT: R 303 MET cc_start: 0.8028 (tmm) cc_final: 0.7806 (tmm) REVERT: R 320 ASN cc_start: 0.8860 (m-40) cc_final: 0.8459 (t0) REVERT: A 31 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8181 (tm130) REVERT: A 35 GLN cc_start: 0.8607 (tt0) cc_final: 0.8028 (tm-30) REVERT: A 204 THR cc_start: 0.8913 (p) cc_final: 0.8697 (p) REVERT: A 239 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8799 (p0) REVERT: A 265 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.9030 (ptm160) REVERT: B 172 GLU cc_start: 0.9116 (tt0) cc_final: 0.8717 (tp30) REVERT: B 215 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8660 (mp0) REVERT: B 268 ASN cc_start: 0.8940 (t0) cc_final: 0.8679 (t0) REVERT: G 18 GLN cc_start: 0.8197 (tp40) cc_final: 0.7479 (tp40) REVERT: G 62 ARG cc_start: 0.5611 (OUTLIER) cc_final: 0.5111 (ptp-170) REVERT: N 38 ARG cc_start: 0.9168 (ptt180) cc_final: 0.8888 (ptt90) REVERT: N 46 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7754 (pt0) REVERT: N 73 ASP cc_start: 0.8024 (t0) cc_final: 0.7695 (t0) REVERT: N 82 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7627 (tm-30) REVERT: N 84 ASN cc_start: 0.7793 (m-40) cc_final: 0.7445 (m110) REVERT: N 87 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7435 (mtmm) REVERT: N 114 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.8918 (p) outliers start: 50 outliers final: 22 residues processed: 195 average time/residue: 0.5203 time to fit residues: 109.0838 Evaluate side-chains 182 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 40.0000 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.0020 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 9 GLN B 88 ASN B 239 ASN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.114710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.070713 restraints weight = 16793.639| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.95 r_work: 0.2738 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9541 Z= 0.122 Angle : 0.600 17.758 12940 Z= 0.302 Chirality : 0.042 0.146 1430 Planarity : 0.004 0.044 1647 Dihedral : 4.452 59.900 1286 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 4.18 % Allowed : 34.43 % Favored : 61.39 % 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: 0.99 (0.26), residues: 1152 helix: 2.16 (0.25), residues: 456 sheet: 0.47 (0.33), residues: 226 loop : -0.76 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.020 0.001 TYR R 145 PHE 0.008 0.001 PHE B 151 TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9535) covalent geometry : angle 0.59966 (12928) SS BOND : bond 0.00166 ( 6) SS BOND : angle 0.73975 ( 12) hydrogen bonds : bond 0.03534 ( 452) hydrogen bonds : angle 4.17023 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8579 (t80) cc_final: 0.8297 (t80) REVERT: R 80 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6855 (t80) REVERT: R 204 MET cc_start: 0.8559 (mmm) cc_final: 0.7909 (mmp) REVERT: R 320 ASN cc_start: 0.8861 (m-40) cc_final: 0.8452 (t0) REVERT: A 31 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8195 (tm130) REVERT: A 35 GLN cc_start: 0.8606 (tt0) cc_final: 0.8006 (tm-30) REVERT: A 204 THR cc_start: 0.8913 (p) cc_final: 0.8693 (p) REVERT: A 239 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8727 (p0) REVERT: A 265 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8998 (ptm160) REVERT: B 172 GLU cc_start: 0.9105 (tt0) cc_final: 0.8719 (tp30) REVERT: B 214 ARG cc_start: 0.9019 (ttm-80) cc_final: 0.8760 (ptm-80) REVERT: B 226 GLU cc_start: 0.8884 (mt-10) cc_final: 0.7781 (mt-10) REVERT: B 268 ASN cc_start: 0.8919 (t0) cc_final: 0.8667 (t0) REVERT: B 301 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8683 (mmtt) REVERT: G 20 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8826 (mttp) REVERT: G 62 ARG cc_start: 0.5694 (OUTLIER) cc_final: 0.5254 (ptp-170) REVERT: N 46 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: N 73 ASP cc_start: 0.8132 (t0) cc_final: 0.7322 (t0) REVERT: N 82 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7726 (tm-30) REVERT: N 87 LYS cc_start: 0.7954 (mttm) cc_final: 0.7598 (mtmt) REVERT: N 114 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.8972 (p) outliers start: 42 outliers final: 22 residues processed: 191 average time/residue: 0.5653 time to fit residues: 115.8045 Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 109 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 23 GLN A 59 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN G 18 GLN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.070619 restraints weight = 16778.285| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.96 r_work: 0.2734 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9541 Z= 0.137 Angle : 0.615 15.245 12940 Z= 0.310 Chirality : 0.042 0.150 1430 Planarity : 0.004 0.054 1647 Dihedral : 4.344 58.606 1285 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 4.78 % Allowed : 33.93 % Favored : 61.29 % 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: 1.03 (0.26), residues: 1152 helix: 2.20 (0.25), residues: 457 sheet: 0.49 (0.33), residues: 226 loop : -0.75 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.056 0.002 TYR R 69 PHE 0.008 0.001 PHE R 280 TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9535) covalent geometry : angle 0.61485 (12928) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.73377 ( 12) hydrogen bonds : bond 0.03560 ( 452) hydrogen bonds : angle 4.14137 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8617 (t80) cc_final: 0.8259 (t80) REVERT: R 80 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6862 (t80) REVERT: R 152 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8638 (m-10) REVERT: R 204 MET cc_start: 0.8542 (mmm) cc_final: 0.7885 (mmp) REVERT: R 320 ASN cc_start: 0.8872 (m-40) cc_final: 0.8481 (t0) REVERT: A 31 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8065 (tm130) REVERT: A 35 GLN cc_start: 0.8597 (tt0) cc_final: 0.7932 (tm-30) REVERT: A 204 THR cc_start: 0.8921 (p) cc_final: 0.8699 (p) REVERT: A 239 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8772 (p0) REVERT: A 265 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.9008 (ptm160) REVERT: A 283 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8066 (ptm160) REVERT: B 172 GLU cc_start: 0.9101 (tt0) cc_final: 0.8723 (tp30) REVERT: B 214 ARG cc_start: 0.9033 (ttm-80) cc_final: 0.8799 (ptm-80) REVERT: B 215 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8906 (tp30) REVERT: B 226 GLU cc_start: 0.8905 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 268 ASN cc_start: 0.8946 (t0) cc_final: 0.8697 (t0) REVERT: B 301 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8708 (mmtt) REVERT: G 46 LYS cc_start: 0.9487 (mtmm) cc_final: 0.8956 (ptpp) REVERT: G 62 ARG cc_start: 0.5790 (OUTLIER) cc_final: 0.5439 (ptp-170) REVERT: N 38 ARG cc_start: 0.9037 (ptm160) cc_final: 0.8810 (ptm-80) REVERT: N 46 GLU cc_start: 0.8239 (tt0) cc_final: 0.7826 (pt0) REVERT: N 73 ASP cc_start: 0.8145 (t0) cc_final: 0.7320 (t0) REVERT: N 82 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7664 (tm-30) REVERT: N 87 LYS cc_start: 0.7841 (mttm) cc_final: 0.7539 (mtmt) REVERT: N 114 THR cc_start: 0.9396 (OUTLIER) cc_final: 0.8985 (p) outliers start: 48 outliers final: 23 residues processed: 195 average time/residue: 0.5780 time to fit residues: 120.8322 Evaluate side-chains 187 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.113346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.069400 restraints weight = 16887.206| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.02 r_work: 0.2709 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9541 Z= 0.161 Angle : 0.629 13.788 12940 Z= 0.321 Chirality : 0.043 0.159 1430 Planarity : 0.004 0.036 1647 Dihedral : 4.368 58.670 1285 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.56 % Favored : 94.27 % Rotamer: Outliers : 4.68 % Allowed : 33.83 % Favored : 61.49 % 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: 1.03 (0.26), residues: 1152 helix: 2.21 (0.25), residues: 456 sheet: 0.54 (0.34), residues: 226 loop : -0.78 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 13 TYR 0.022 0.002 TYR R 145 PHE 0.010 0.001 PHE N 108 TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9535) covalent geometry : angle 0.62851 (12928) SS BOND : bond 0.00365 ( 6) SS BOND : angle 0.99045 ( 12) hydrogen bonds : bond 0.03661 ( 452) hydrogen bonds : angle 4.17531 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8571 (t80) cc_final: 0.8233 (t80) REVERT: R 71 CYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8125 (m) REVERT: R 204 MET cc_start: 0.8579 (mmm) cc_final: 0.7951 (mmp) REVERT: R 320 ASN cc_start: 0.8828 (m-40) cc_final: 0.8470 (t0) REVERT: A 31 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8072 (tm130) REVERT: A 265 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.9013 (ptm160) REVERT: A 283 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8051 (ptm160) REVERT: A 392 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8697 (mt-10) REVERT: B 172 GLU cc_start: 0.9097 (tt0) cc_final: 0.8697 (tp30) REVERT: B 215 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8707 (mp0) REVERT: B 268 ASN cc_start: 0.9009 (t0) cc_final: 0.8766 (t0) REVERT: B 301 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8653 (mmtt) REVERT: G 20 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8779 (mttp) REVERT: G 29 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8441 (mmmt) REVERT: G 32 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8915 (tppp) REVERT: G 62 ARG cc_start: 0.5804 (OUTLIER) cc_final: 0.5462 (ptp-170) REVERT: N 38 ARG cc_start: 0.9006 (ptm160) cc_final: 0.8748 (ptm-80) REVERT: N 46 GLU cc_start: 0.8264 (tt0) cc_final: 0.7761 (pt0) REVERT: N 73 ASP cc_start: 0.8132 (t0) cc_final: 0.7277 (t0) REVERT: N 76 LYS cc_start: 0.9463 (mtpm) cc_final: 0.9194 (mtpp) REVERT: N 82 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7746 (mm-40) REVERT: N 87 LYS cc_start: 0.7864 (mttm) cc_final: 0.7553 (mtmt) REVERT: N 114 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9002 (p) outliers start: 47 outliers final: 30 residues processed: 195 average time/residue: 0.5881 time to fit residues: 122.8881 Evaluate side-chains 193 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 4 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN G 18 GLN N 3 GLN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.114099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.069936 restraints weight = 16604.862| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.98 r_work: 0.2729 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9541 Z= 0.139 Angle : 0.632 12.716 12940 Z= 0.321 Chirality : 0.042 0.168 1430 Planarity : 0.004 0.046 1647 Dihedral : 4.375 59.502 1285 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.86 % Favored : 94.97 % Rotamer: Outliers : 4.88 % Allowed : 33.73 % Favored : 61.39 % 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: 1.00 (0.26), residues: 1152 helix: 2.16 (0.25), residues: 457 sheet: 0.47 (0.34), residues: 227 loop : -0.75 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 105 TYR 0.019 0.001 TYR P 19 PHE 0.009 0.001 PHE R 367 TRP 0.012 0.001 TRP B 339 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9535) covalent geometry : angle 0.63147 (12928) SS BOND : bond 0.00199 ( 6) SS BOND : angle 1.14122 ( 12) hydrogen bonds : bond 0.03566 ( 452) hydrogen bonds : angle 4.16955 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8585 (t80) cc_final: 0.8315 (t80) REVERT: R 204 MET cc_start: 0.8583 (mmm) cc_final: 0.7951 (mmp) REVERT: R 320 ASN cc_start: 0.8865 (m-40) cc_final: 0.8540 (t0) REVERT: A 31 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8086 (tm130) REVERT: A 204 THR cc_start: 0.8975 (p) cc_final: 0.8754 (p) REVERT: A 239 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8774 (p0) REVERT: A 265 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.9029 (ptm160) REVERT: A 283 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8075 (ptm160) REVERT: A 392 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8698 (mt-10) REVERT: B 172 GLU cc_start: 0.9095 (tt0) cc_final: 0.8737 (tp30) REVERT: B 215 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9069 (tp30) REVERT: B 226 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8061 (mt-10) REVERT: B 268 ASN cc_start: 0.9008 (t0) cc_final: 0.8773 (t0) REVERT: B 301 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8669 (mmtt) REVERT: G 29 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8442 (mmmt) REVERT: G 32 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8881 (tppp) REVERT: G 62 ARG cc_start: 0.5834 (OUTLIER) cc_final: 0.5489 (ptp-170) REVERT: N 46 GLU cc_start: 0.8271 (tt0) cc_final: 0.7957 (pt0) REVERT: N 73 ASP cc_start: 0.8165 (t0) cc_final: 0.7331 (t0) REVERT: N 76 LYS cc_start: 0.9469 (mtpm) cc_final: 0.9208 (mtpp) REVERT: N 82 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: N 87 LYS cc_start: 0.7846 (mttm) cc_final: 0.7517 (mtmt) REVERT: N 114 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9033 (p) outliers start: 49 outliers final: 28 residues processed: 197 average time/residue: 0.5749 time to fit residues: 121.3192 Evaluate side-chains 191 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN G 18 GLN N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.114417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.070955 restraints weight = 16653.850| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.94 r_work: 0.2745 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9541 Z= 0.133 Angle : 0.661 14.481 12940 Z= 0.333 Chirality : 0.043 0.187 1430 Planarity : 0.004 0.053 1647 Dihedral : 4.326 56.544 1285 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 3.68 % Allowed : 35.32 % Favored : 61.00 % 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: 0.96 (0.26), residues: 1152 helix: 2.14 (0.25), residues: 457 sheet: 0.49 (0.34), residues: 227 loop : -0.80 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 214 TYR 0.022 0.001 TYR R 145 PHE 0.010 0.001 PHE R 367 TRP 0.011 0.001 TRP A 234 HIS 0.007 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9535) covalent geometry : angle 0.65918 (12928) SS BOND : bond 0.00181 ( 6) SS BOND : angle 1.54108 ( 12) hydrogen bonds : bond 0.03526 ( 452) hydrogen bonds : angle 4.17044 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8612 (t80) cc_final: 0.8289 (t80) REVERT: R 204 MET cc_start: 0.8588 (mmm) cc_final: 0.7951 (mmp) REVERT: R 320 ASN cc_start: 0.8878 (m-40) cc_final: 0.8568 (t0) REVERT: A 31 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8087 (tm130) REVERT: A 239 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8759 (p0) REVERT: A 265 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.9028 (ptm160) REVERT: A 283 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8081 (ptm160) REVERT: A 392 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8686 (mt-10) REVERT: B 172 GLU cc_start: 0.9094 (tt0) cc_final: 0.8740 (tp30) REVERT: B 226 GLU cc_start: 0.8673 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 268 ASN cc_start: 0.8997 (t0) cc_final: 0.8778 (t0) REVERT: B 301 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8691 (mmtm) REVERT: G 29 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8466 (mmmt) REVERT: G 32 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8999 (tppp) REVERT: G 62 ARG cc_start: 0.5833 (OUTLIER) cc_final: 0.5499 (ptp-170) REVERT: N 38 ARG cc_start: 0.8981 (ptm160) cc_final: 0.8746 (ptm-80) REVERT: N 45 LEU cc_start: 0.9060 (mt) cc_final: 0.8804 (mt) REVERT: N 46 GLU cc_start: 0.8239 (tt0) cc_final: 0.7845 (pt0) REVERT: N 73 ASP cc_start: 0.8165 (t0) cc_final: 0.7332 (t0) REVERT: N 76 LYS cc_start: 0.9468 (mtpm) cc_final: 0.9207 (mtpp) REVERT: N 82 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7609 (tm-30) REVERT: N 87 LYS cc_start: 0.7861 (mttm) cc_final: 0.7565 (mtmt) REVERT: N 114 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9038 (p) outliers start: 37 outliers final: 27 residues processed: 191 average time/residue: 0.5387 time to fit residues: 110.3481 Evaluate side-chains 193 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 239 ASN G 18 GLN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.114217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.070296 restraints weight = 16732.448| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.98 r_work: 0.2732 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9541 Z= 0.148 Angle : 0.690 14.247 12940 Z= 0.344 Chirality : 0.043 0.193 1430 Planarity : 0.004 0.056 1647 Dihedral : 4.375 59.364 1285 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 3.68 % Allowed : 35.62 % Favored : 60.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.26), residues: 1152 helix: 2.11 (0.25), residues: 457 sheet: 0.51 (0.34), residues: 227 loop : -0.84 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG R 48 TYR 0.019 0.001 TYR P 19 PHE 0.010 0.001 PHE R 367 TRP 0.011 0.001 TRP R 120 HIS 0.005 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9535) covalent geometry : angle 0.68910 (12928) SS BOND : bond 0.00185 ( 6) SS BOND : angle 1.32231 ( 12) hydrogen bonds : bond 0.03587 ( 452) hydrogen bonds : angle 4.17562 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8609 (t80) cc_final: 0.8286 (t80) REVERT: R 152 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: R 204 MET cc_start: 0.8590 (mmm) cc_final: 0.7956 (mmp) REVERT: R 320 ASN cc_start: 0.8884 (m-40) cc_final: 0.8573 (t0) REVERT: A 31 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8091 (tm130) REVERT: A 239 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8782 (p0) REVERT: A 265 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.9030 (ptm160) REVERT: A 283 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8060 (ptm160) REVERT: A 392 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8692 (mt-10) REVERT: B 20 ASP cc_start: 0.9237 (m-30) cc_final: 0.8893 (m-30) REVERT: B 172 GLU cc_start: 0.9095 (tt0) cc_final: 0.8747 (tp30) REVERT: B 226 GLU cc_start: 0.8690 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 268 ASN cc_start: 0.9024 (t0) cc_final: 0.8797 (t0) REVERT: B 301 LYS cc_start: 0.9066 (mtpp) cc_final: 0.8754 (mmtt) REVERT: G 29 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8457 (mmmt) REVERT: G 32 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8978 (tppp) REVERT: G 62 ARG cc_start: 0.5843 (OUTLIER) cc_final: 0.5507 (ptp-170) REVERT: N 38 ARG cc_start: 0.8935 (ptm160) cc_final: 0.8700 (ptm-80) REVERT: N 46 GLU cc_start: 0.8274 (tt0) cc_final: 0.7903 (pt0) REVERT: N 73 ASP cc_start: 0.8171 (t0) cc_final: 0.7341 (t0) REVERT: N 76 LYS cc_start: 0.9472 (mtpm) cc_final: 0.9206 (mtpp) REVERT: N 82 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7740 (mm-40) REVERT: N 87 LYS cc_start: 0.7843 (mttm) cc_final: 0.7492 (mtmm) REVERT: N 114 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9048 (p) outliers start: 37 outliers final: 25 residues processed: 185 average time/residue: 0.5486 time to fit residues: 108.8322 Evaluate side-chains 190 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.114490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.070739 restraints weight = 16569.583| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.98 r_work: 0.2741 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9541 Z= 0.135 Angle : 0.682 13.751 12940 Z= 0.341 Chirality : 0.043 0.185 1430 Planarity : 0.004 0.054 1647 Dihedral : 4.375 59.965 1285 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % Rotamer: Outliers : 2.99 % Allowed : 36.42 % Favored : 60.60 % 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: 0.88 (0.26), residues: 1152 helix: 2.07 (0.25), residues: 457 sheet: 0.51 (0.34), residues: 227 loop : -0.90 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 48 TYR 0.023 0.001 TYR R 145 PHE 0.011 0.001 PHE R 367 TRP 0.013 0.001 TRP R 120 HIS 0.005 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9535) covalent geometry : angle 0.68147 (12928) SS BOND : bond 0.00156 ( 6) SS BOND : angle 1.27531 ( 12) hydrogen bonds : bond 0.03566 ( 452) hydrogen bonds : angle 4.15903 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3622.32 seconds wall clock time: 62 minutes 30.53 seconds (3750.53 seconds total)