Starting phenix.real_space_refine on Thu Jan 16 09:18:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivg_60927/01_2025/9ivg_60927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivg_60927/01_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_60927/01_2025/9ivg_60927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivg_60927/01_2025/9ivg_60927.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivg_60927/01_2025/9ivg_60927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivg_60927/01_2025/9ivg_60927.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.56, per 1000 atoms: 0.60 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 2.72 Time building geometry restraints manager: 2.79 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- 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 9535 Z= 0.208 Angle : 0.556 8.418 12928 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 : 7.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 TRP 0.033 0.002 TRP R 39 HIS 0.003 0.001 HIS A 220 PHE 0.012 0.001 PHE B 253 TYR 0.024 0.001 TYR R 148 ARG 0.006 0.000 ARG B 219 *********************** 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 : 1.050 Fit side-chains 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: 0.7878 (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: 0.7940 (tp40) REVERT: G 20 LYS cc_start: 0.9284 (mttt) cc_final: 0.9070 (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: 16 residues processed: 224 average time/residue: 1.2451 time to fit residues: 298.1701 Evaluate side-chains 179 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 228 LEU 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 96 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.113841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.069397 restraints weight = 16646.784| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.00 r_work: 0.2685 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9535 Z= 0.269 Angle : 0.620 9.269 12928 Z= 0.321 Chirality : 0.043 0.185 1430 Planarity : 0.004 0.045 1647 Dihedral : 5.538 52.161 1306 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 5.27 % Allowed : 31.24 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1152 helix: 1.91 (0.25), residues: 455 sheet: 0.51 (0.32), residues: 227 loop : -0.75 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 39 HIS 0.008 0.001 HIS R 99 PHE 0.011 0.001 PHE A 238 TYR 0.015 0.001 TYR R 148 ARG 0.009 0.001 ARG G 13 *********************** 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 236 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8560 (t80) cc_final: 0.8169 (t80) REVERT: R 204 MET cc_start: 0.8541 (mmm) cc_final: 0.7905 (mmp) REVERT: A 35 GLN cc_start: 0.8694 (tt0) cc_final: 0.8086 (tm-30) REVERT: B 10 GLU cc_start: 0.8875 (tp30) cc_final: 0.8647 (tp30) REVERT: B 197 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8375 (mmm-85) REVERT: B 226 GLU cc_start: 0.8945 (mt-10) cc_final: 0.7929 (mt-10) REVERT: B 260 GLU cc_start: 0.8675 (pt0) cc_final: 0.8146 (tt0) REVERT: B 262 MET cc_start: 0.8577 (mmm) cc_final: 0.8319 (tpp) REVERT: B 268 ASN cc_start: 0.8878 (t0) cc_final: 0.8604 (t0) REVERT: G 13 ARG cc_start: 0.8875 (ttp80) cc_final: 0.8667 (ttp80) REVERT: G 18 GLN cc_start: 0.8105 (tp40) cc_final: 0.7502 (tp40) REVERT: G 29 LYS cc_start: 0.8697 (mmpt) cc_final: 0.8405 (mmpt) REVERT: G 62 ARG cc_start: 0.5335 (OUTLIER) cc_final: 0.4885 (ptp-170) REVERT: N 38 ARG cc_start: 0.9134 (ptt180) cc_final: 0.8692 (ptt90) REVERT: N 46 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: N 73 ASP cc_start: 0.7742 (t0) cc_final: 0.7429 (t0) REVERT: N 82 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7711 (mm-40) REVERT: N 84 ASN cc_start: 0.7717 (m-40) cc_final: 0.7448 (m110) REVERT: N 114 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8832 (p) outliers start: 53 outliers final: 21 residues processed: 221 average time/residue: 1.1126 time to fit residues: 264.5660 Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 279 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL 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 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 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 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 74 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 6 optimal weight: 0.0770 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.071636 restraints weight = 16737.793| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.99 r_work: 0.2749 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9535 Z= 0.162 Angle : 0.583 8.805 12928 Z= 0.299 Chirality : 0.042 0.157 1430 Planarity : 0.004 0.038 1647 Dihedral : 4.533 48.981 1288 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.14 % Rotamer: Outliers : 4.98 % Allowed : 33.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1152 helix: 2.14 (0.25), residues: 448 sheet: 0.51 (0.33), residues: 226 loop : -0.73 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.003 0.000 HIS R 99 PHE 0.008 0.001 PHE A 212 TYR 0.018 0.001 TYR R 145 ARG 0.006 0.000 ARG R 64 *********************** 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: 50 poor density : 172 time to evaluate : 1.081 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: 0.8556 (t80) cc_final: 0.8206 (t80) REVERT: R 204 MET cc_start: 0.8539 (mmm) cc_final: 0.7890 (mmp) REVERT: R 303 MET cc_start: 0.8078 (tmm) cc_final: 0.7845 (tmm) REVERT: A 31 GLN cc_start: 0.8729 (tp40) cc_final: 0.8246 (tm130) REVERT: A 35 GLN cc_start: 0.8642 (tt0) cc_final: 0.8050 (tm-30) REVERT: A 204 THR cc_start: 0.8912 (p) cc_final: 0.8700 (p) REVERT: A 239 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8786 (p0) REVERT: B 226 GLU cc_start: 0.8931 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 268 ASN cc_start: 0.8908 (t0) cc_final: 0.8641 (t0) REVERT: G 18 GLN cc_start: 0.8168 (tp40) cc_final: 0.7466 (tp40) REVERT: G 20 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8827 (mttp) REVERT: G 29 LYS cc_start: 0.8713 (mmpt) cc_final: 0.8356 (mmmm) REVERT: G 62 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.5192 (ptp-170) REVERT: N 38 ARG cc_start: 0.9189 (ptt180) cc_final: 0.8791 (ptt90) REVERT: N 46 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: N 73 ASP cc_start: 0.7908 (t0) cc_final: 0.7565 (t0) REVERT: N 82 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7668 (tm-30) REVERT: N 84 ASN cc_start: 0.7799 (m-40) cc_final: 0.7376 (m110) REVERT: N 114 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.8929 (p) outliers start: 50 outliers final: 22 residues processed: 206 average time/residue: 1.1053 time to fit residues: 245.0482 Evaluate side-chains 179 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 142 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 ILE 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 B residue 29 THR Chi-restraints excluded: chain B residue 189 SER 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 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0070 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 12 optimal weight: 0.0070 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- 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 N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.071288 restraints weight = 16570.519| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.03 r_work: 0.2738 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9535 Z= 0.173 Angle : 0.574 9.114 12928 Z= 0.292 Chirality : 0.041 0.148 1430 Planarity : 0.003 0.037 1647 Dihedral : 4.274 47.667 1286 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 4.88 % Allowed : 32.64 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1152 helix: 2.12 (0.25), residues: 457 sheet: 0.50 (0.33), residues: 226 loop : -0.72 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.002 0.000 HIS A 220 PHE 0.009 0.001 PHE R 280 TYR 0.020 0.001 TYR R 145 ARG 0.009 0.000 ARG G 13 *********************** 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 210 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8546 (t80) cc_final: 0.8198 (t80) REVERT: R 152 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8584 (m-10) REVERT: R 204 MET cc_start: 0.8523 (mmm) cc_final: 0.7867 (mmp) REVERT: R 303 MET cc_start: 0.8047 (tmm) cc_final: 0.7822 (tmm) REVERT: R 320 ASN cc_start: 0.8839 (m-40) cc_final: 0.8430 (t0) REVERT: A 31 GLN cc_start: 0.8662 (tp40) cc_final: 0.8217 (tm130) REVERT: A 35 GLN cc_start: 0.8598 (tt0) cc_final: 0.7978 (tm-30) REVERT: A 204 THR cc_start: 0.8866 (p) cc_final: 0.8619 (p) REVERT: A 265 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.9002 (ptm160) REVERT: B 214 ARG cc_start: 0.9101 (ttm-80) cc_final: 0.8734 (ptm-80) REVERT: B 226 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8001 (mt-10) REVERT: B 262 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8341 (mtp) REVERT: B 268 ASN cc_start: 0.8925 (t0) cc_final: 0.8662 (t0) REVERT: G 18 GLN cc_start: 0.8186 (tp40) cc_final: 0.7434 (tp40) REVERT: G 29 LYS cc_start: 0.8679 (mmpt) cc_final: 0.8334 (mmmm) REVERT: G 62 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.5013 (ptp-170) REVERT: N 38 ARG cc_start: 0.9159 (ptt180) cc_final: 0.8714 (ptt90) REVERT: N 46 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: N 73 ASP cc_start: 0.8023 (t0) cc_final: 0.7688 (t0) REVERT: N 82 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7575 (tm-30) REVERT: N 84 ASN cc_start: 0.7815 (m-40) cc_final: 0.7463 (m110) REVERT: N 87 LYS cc_start: 0.7663 (mtmt) cc_final: 0.7400 (mtmt) REVERT: N 114 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9026 (p) outliers start: 49 outliers final: 25 residues processed: 199 average time/residue: 1.0836 time to fit residues: 232.5769 Evaluate side-chains 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 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 152 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 282 VAL 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 B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 258 ASP 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 57 SER 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 104 THR 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 75 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 239 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.114288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.069902 restraints weight = 16641.729| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.98 r_work: 0.2718 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 9535 Z= 0.279 Angle : 0.606 11.325 12928 Z= 0.313 Chirality : 0.043 0.260 1430 Planarity : 0.004 0.049 1647 Dihedral : 4.102 48.800 1285 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 4.28 % Allowed : 33.73 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1152 helix: 2.12 (0.25), residues: 458 sheet: 0.46 (0.33), residues: 227 loop : -0.74 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS R 171 PHE 0.009 0.001 PHE B 151 TYR 0.020 0.001 TYR R 145 ARG 0.006 0.000 ARG R 48 *********************** 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 201 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 1.064 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: 0.8214 (t80) REVERT: R 80 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6830 (t80) REVERT: R 204 MET cc_start: 0.8565 (mmm) cc_final: 0.7915 (mmp) REVERT: R 303 MET cc_start: 0.8125 (tmm) cc_final: 0.7892 (tmm) REVERT: R 320 ASN cc_start: 0.8894 (m-40) cc_final: 0.8473 (t0) REVERT: A 31 GLN cc_start: 0.8686 (tp40) cc_final: 0.8136 (tm130) REVERT: A 35 GLN cc_start: 0.8614 (tt0) cc_final: 0.7954 (tm-30) REVERT: A 204 THR cc_start: 0.8920 (p) cc_final: 0.8706 (p) REVERT: A 265 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.9020 (ptm160) REVERT: B 214 ARG cc_start: 0.8987 (ttm-80) cc_final: 0.8759 (ptm-80) REVERT: B 215 GLU cc_start: 0.9132 (tp30) cc_final: 0.8807 (mm-30) REVERT: B 226 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 262 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8300 (mtp) REVERT: B 268 ASN cc_start: 0.8928 (t0) cc_final: 0.8662 (t0) REVERT: B 301 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8700 (mmtt) REVERT: G 18 GLN cc_start: 0.8118 (tp40) cc_final: 0.7489 (tp40) REVERT: G 20 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8826 (mttp) REVERT: G 46 LYS cc_start: 0.9498 (mtmm) cc_final: 0.8956 (ptpp) REVERT: G 62 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.5136 (ptp-170) REVERT: N 46 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: N 73 ASP cc_start: 0.8130 (t0) cc_final: 0.7326 (t0) REVERT: N 82 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7788 (mm-40) REVERT: N 84 ASN cc_start: 0.7897 (m-40) cc_final: 0.7688 (m110) REVERT: N 87 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7395 (mtmt) outliers start: 43 outliers final: 26 residues processed: 188 average time/residue: 1.1872 time to fit residues: 240.4033 Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 229 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 279 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 265 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER 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 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 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 109 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 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 A 59 GLN A 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.113755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.069697 restraints weight = 16512.425| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.96 r_work: 0.2721 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9535 Z= 0.250 Angle : 0.614 9.379 12928 Z= 0.315 Chirality : 0.043 0.152 1430 Planarity : 0.004 0.039 1647 Dihedral : 4.118 49.211 1284 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 4.98 % Allowed : 33.33 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1152 helix: 2.12 (0.25), residues: 458 sheet: 0.41 (0.33), residues: 229 loop : -0.75 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS R 171 PHE 0.008 0.001 PHE A 212 TYR 0.059 0.002 TYR R 69 ARG 0.007 0.000 ARG N 105 *********************** 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: 50 poor density : 159 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8559 (t80) cc_final: 0.8243 (t80) REVERT: R 80 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6840 (t80) REVERT: R 204 MET cc_start: 0.8574 (mmm) cc_final: 0.7926 (mmp) REVERT: R 320 ASN cc_start: 0.8865 (m-40) cc_final: 0.8476 (t0) REVERT: A 31 GLN cc_start: 0.8660 (tp40) cc_final: 0.8091 (tm130) REVERT: A 35 GLN cc_start: 0.8585 (tt0) cc_final: 0.7929 (tm-30) REVERT: A 204 THR cc_start: 0.8961 (p) cc_final: 0.8745 (p) REVERT: A 265 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.9002 (ptm160) REVERT: A 283 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7993 (ptm160) REVERT: A 392 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8684 (mt-10) REVERT: B 215 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8532 (mp0) REVERT: B 262 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8532 (mtp) REVERT: B 268 ASN cc_start: 0.8990 (t0) cc_final: 0.8741 (t0) REVERT: B 301 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8640 (mmtt) REVERT: G 62 ARG cc_start: 0.5685 (OUTLIER) cc_final: 0.5280 (ptp-170) REVERT: N 38 ARG cc_start: 0.9028 (ptm160) cc_final: 0.8767 (ptm-80) REVERT: N 46 GLU cc_start: 0.8247 (tt0) cc_final: 0.7736 (pt0) REVERT: N 73 ASP cc_start: 0.8167 (t0) cc_final: 0.7357 (t0) REVERT: N 82 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7642 (tm-30) REVERT: N 84 ASN cc_start: 0.7921 (m-40) cc_final: 0.7618 (m110) REVERT: N 87 LYS cc_start: 0.7679 (mtmt) cc_final: 0.7421 (mtmt) REVERT: N 114 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9071 (p) outliers start: 50 outliers final: 26 residues processed: 197 average time/residue: 1.1949 time to fit residues: 252.1871 Evaluate side-chains 186 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 413 PHE Chi-restraints excluded: chain A residue 200 THR 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 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 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU 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 62 ARG Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR 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 108 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.114909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.070985 restraints weight = 16710.360| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.97 r_work: 0.2750 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9535 Z= 0.204 Angle : 0.621 10.190 12928 Z= 0.319 Chirality : 0.042 0.159 1430 Planarity : 0.004 0.039 1647 Dihedral : 4.251 48.450 1284 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 4.58 % Allowed : 33.73 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1152 helix: 2.16 (0.25), residues: 459 sheet: 0.41 (0.33), residues: 228 loop : -0.82 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 171 PHE 0.009 0.001 PHE R 367 TYR 0.021 0.001 TYR R 145 ARG 0.012 0.000 ARG G 13 *********************** 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 210 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 1.063 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: 0.8215 (t80) REVERT: R 71 CYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8132 (m) REVERT: R 152 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8657 (m-10) REVERT: R 204 MET cc_start: 0.8583 (mmm) cc_final: 0.7946 (mmp) REVERT: R 320 ASN cc_start: 0.8881 (m-40) cc_final: 0.8511 (t0) REVERT: A 31 GLN cc_start: 0.8680 (tp40) cc_final: 0.8081 (tm130) REVERT: A 35 GLN cc_start: 0.8559 (tt0) cc_final: 0.7894 (tm-30) REVERT: A 204 THR cc_start: 0.8953 (p) cc_final: 0.8733 (p) REVERT: A 239 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8774 (p0) REVERT: A 265 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8970 (ptm160) REVERT: A 283 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7970 (ptm160) REVERT: A 392 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8678 (mt-10) REVERT: B 226 GLU cc_start: 0.8781 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 268 ASN cc_start: 0.8986 (t0) cc_final: 0.8741 (t0) REVERT: B 301 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8698 (mmtt) REVERT: G 17 GLU cc_start: 0.9114 (tp30) cc_final: 0.8850 (tp30) REVERT: G 20 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8808 (ttmm) REVERT: G 46 LYS cc_start: 0.9481 (mtmm) cc_final: 0.8928 (ptpp) REVERT: G 62 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.5456 (ptp-170) REVERT: N 73 ASP cc_start: 0.8180 (t0) cc_final: 0.7339 (t0) REVERT: N 76 LYS cc_start: 0.9468 (mtpm) cc_final: 0.9194 (mtpp) REVERT: N 82 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7683 (tm-30) REVERT: N 84 ASN cc_start: 0.7880 (m-40) cc_final: 0.7595 (m110) REVERT: N 87 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7445 (mtmt) REVERT: N 114 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9075 (p) outliers start: 46 outliers final: 21 residues processed: 200 average time/residue: 1.1176 time to fit residues: 240.3728 Evaluate side-chains 187 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 44 ARG 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 152 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE 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 173 THR Chi-restraints excluded: chain B residue 189 SER 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 62 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR 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 9 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 28 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 340 ASN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.071591 restraints weight = 16771.491| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.98 r_work: 0.2760 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9535 Z= 0.200 Angle : 0.636 10.103 12928 Z= 0.326 Chirality : 0.042 0.163 1430 Planarity : 0.004 0.051 1647 Dihedral : 4.240 47.616 1284 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 4.08 % Allowed : 34.33 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1152 helix: 2.13 (0.25), residues: 459 sheet: 0.39 (0.33), residues: 226 loop : -0.87 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.008 0.001 HIS R 171 PHE 0.009 0.001 PHE R 367 TYR 0.019 0.001 TYR P 19 ARG 0.017 0.001 ARG R 48 *********************** 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 205 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.100 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: 0.8545 (t80) cc_final: 0.8294 (t80) REVERT: R 71 CYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8106 (m) REVERT: R 152 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8643 (m-10) REVERT: R 204 MET cc_start: 0.8584 (mmm) cc_final: 0.7949 (mmp) REVERT: R 320 ASN cc_start: 0.8870 (m-40) cc_final: 0.8504 (t0) REVERT: A 31 GLN cc_start: 0.8682 (tp40) cc_final: 0.8079 (tm130) REVERT: A 204 THR cc_start: 0.8943 (p) cc_final: 0.8690 (p) REVERT: A 239 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8767 (p0) REVERT: A 265 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8969 (ptm160) REVERT: A 317 ARG cc_start: 0.9224 (mtm-85) cc_final: 0.8939 (ptp-110) REVERT: A 392 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8687 (mt-10) REVERT: B 226 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8173 (mt-10) REVERT: B 268 ASN cc_start: 0.9022 (t0) cc_final: 0.8773 (t0) REVERT: B 301 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8640 (mmtt) REVERT: G 17 GLU cc_start: 0.9099 (tp30) cc_final: 0.8828 (tp30) REVERT: G 20 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8787 (ttmm) REVERT: G 46 LYS cc_start: 0.9465 (mtmm) cc_final: 0.8930 (ptpp) REVERT: G 62 ARG cc_start: 0.5851 (OUTLIER) cc_final: 0.5501 (ptp-170) REVERT: N 45 LEU cc_start: 0.9091 (mt) cc_final: 0.8868 (mt) REVERT: N 46 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: N 73 ASP cc_start: 0.8172 (t0) cc_final: 0.7333 (t0) REVERT: N 76 LYS cc_start: 0.9464 (mtpm) cc_final: 0.9198 (mtpp) REVERT: N 82 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7698 (tm-30) REVERT: N 84 ASN cc_start: 0.7895 (m-40) cc_final: 0.7610 (m110) REVERT: N 87 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7441 (mtmt) REVERT: N 114 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9090 (p) outliers start: 41 outliers final: 26 residues processed: 196 average time/residue: 1.1644 time to fit residues: 244.5671 Evaluate side-chains 192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 44 ARG 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 229 VAL 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 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 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER 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 B residue 338 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 4 LEU 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 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 239 ASN G 18 GLN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.115150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.071574 restraints weight = 16734.700| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.97 r_work: 0.2758 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9535 Z= 0.217 Angle : 0.660 11.866 12928 Z= 0.337 Chirality : 0.043 0.187 1430 Planarity : 0.004 0.053 1647 Dihedral : 4.215 48.071 1284 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.86 % Favored : 94.97 % Rotamer: Outliers : 3.78 % Allowed : 35.32 % Favored : 60.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1152 helix: 2.00 (0.25), residues: 465 sheet: 0.40 (0.34), residues: 227 loop : -0.92 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 120 HIS 0.006 0.001 HIS R 171 PHE 0.009 0.001 PHE R 367 TYR 0.024 0.001 TYR R 145 ARG 0.013 0.001 ARG B 214 *********************** 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 199 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 1.098 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: 0.8590 (t80) cc_final: 0.8303 (t80) REVERT: P 21 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8968 (tp30) REVERT: R 152 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8606 (m-10) REVERT: R 204 MET cc_start: 0.8589 (mmm) cc_final: 0.7949 (mmp) REVERT: R 303 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7344 (tpt) REVERT: R 320 ASN cc_start: 0.8874 (m-40) cc_final: 0.8509 (t0) REVERT: A 31 GLN cc_start: 0.8711 (tp40) cc_final: 0.8092 (tm130) REVERT: A 204 THR cc_start: 0.8949 (p) cc_final: 0.8745 (p) REVERT: A 239 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8772 (p0) REVERT: A 265 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8963 (ptm160) REVERT: A 317 ARG cc_start: 0.9227 (mtm-85) cc_final: 0.8946 (ptp-110) REVERT: A 392 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8688 (mt-10) REVERT: B 226 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8189 (mt-10) REVERT: B 268 ASN cc_start: 0.9015 (t0) cc_final: 0.8784 (t0) REVERT: B 301 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8661 (mmtt) REVERT: G 20 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8798 (ttmm) REVERT: G 62 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5547 (ptp-170) REVERT: N 38 ARG cc_start: 0.9013 (ptm160) cc_final: 0.8792 (ptm-80) REVERT: N 45 LEU cc_start: 0.9048 (mt) cc_final: 0.8803 (mt) REVERT: N 46 GLU cc_start: 0.8313 (tt0) cc_final: 0.8001 (pt0) REVERT: N 73 ASP cc_start: 0.8121 (t0) cc_final: 0.7319 (t0) REVERT: N 76 LYS cc_start: 0.9461 (mtpm) cc_final: 0.9203 (mtpp) REVERT: N 82 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7591 (tm-30) REVERT: N 84 ASN cc_start: 0.7920 (m-40) cc_final: 0.7645 (m110) REVERT: N 108 PHE cc_start: 0.8287 (m-80) cc_final: 0.7748 (m-80) REVERT: N 114 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9106 (p) outliers start: 38 outliers final: 28 residues processed: 190 average time/residue: 1.1489 time to fit residues: 234.1666 Evaluate side-chains 192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 44 ARG 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 229 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 413 PHE 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 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER 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 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 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 G 59 ASN N 77 ASN N 120 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 = 0.114323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.070604 restraints weight = 16887.233| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.98 r_work: 0.2738 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9535 Z= 0.256 Angle : 0.688 11.464 12928 Z= 0.349 Chirality : 0.044 0.222 1430 Planarity : 0.004 0.050 1647 Dihedral : 4.300 48.623 1284 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 3.48 % Allowed : 35.62 % Favored : 60.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1152 helix: 2.00 (0.25), residues: 465 sheet: 0.34 (0.34), residues: 225 loop : -0.96 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 120 HIS 0.005 0.001 HIS R 171 PHE 0.010 0.001 PHE R 367 TYR 0.018 0.001 TYR P 19 ARG 0.027 0.001 ARG R 48 ********************** 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 190 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8588 (t80) cc_final: 0.8284 (t80) REVERT: P 21 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8984 (tp30) REVERT: R 204 MET cc_start: 0.8594 (mmm) cc_final: 0.7960 (mmp) REVERT: R 320 ASN cc_start: 0.8911 (m-40) cc_final: 0.8550 (t0) REVERT: A 31 GLN cc_start: 0.8708 (tp40) cc_final: 0.8092 (tm130) REVERT: A 239 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8818 (p0) REVERT: A 265 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8990 (ptm160) REVERT: B 20 ASP cc_start: 0.9242 (m-30) cc_final: 0.8915 (m-30) REVERT: B 226 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 268 ASN cc_start: 0.9024 (t0) cc_final: 0.8799 (t0) REVERT: B 301 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8590 (mmtt) REVERT: G 20 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8789 (ttmm) REVERT: G 46 LYS cc_start: 0.9421 (mtmm) cc_final: 0.8870 (ptpp) REVERT: G 62 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5561 (ptp-170) REVERT: N 38 ARG cc_start: 0.8997 (ptm160) cc_final: 0.8796 (ptm-80) REVERT: N 46 GLU cc_start: 0.8276 (tt0) cc_final: 0.7974 (pt0) REVERT: N 73 ASP cc_start: 0.8166 (t0) cc_final: 0.7331 (t0) REVERT: N 76 LYS cc_start: 0.9478 (mtpm) cc_final: 0.9216 (mtpp) REVERT: N 82 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7731 (mm-40) REVERT: N 114 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9125 (p) outliers start: 35 outliers final: 26 residues processed: 184 average time/residue: 1.1373 time to fit residues: 225.7134 Evaluate side-chains 183 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 230 PHE 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 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 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER 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 G residue 50 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR 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 69 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN G 18 GLN G 59 ASN N 77 ASN N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.114998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071244 restraints weight = 16784.795| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.99 r_work: 0.2749 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9535 Z= 0.237 Angle : 0.699 12.812 12928 Z= 0.353 Chirality : 0.043 0.179 1430 Planarity : 0.004 0.056 1647 Dihedral : 4.325 48.308 1284 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 3.18 % Allowed : 36.12 % Favored : 60.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1152 helix: 1.95 (0.25), residues: 465 sheet: 0.33 (0.34), residues: 225 loop : -0.96 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 120 HIS 0.004 0.001 HIS R 171 PHE 0.012 0.001 PHE R 367 TYR 0.023 0.001 TYR R 145 ARG 0.025 0.001 ARG R 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6727.53 seconds wall clock time: 119 minutes 41.08 seconds (7181.08 seconds total)