Starting phenix.real_space_refine on Mon May 12 20:30:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivg_60927/05_2025/9ivg_60927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivg_60927/05_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_60927/05_2025/9ivg_60927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivg_60927/05_2025/9ivg_60927.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivg_60927/05_2025/9ivg_60927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivg_60927/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.23, per 1000 atoms: 0.56 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: 2.23 Conformation dependent library (CDL) restraints added in 1.0 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: 0.96 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: 2.41 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3041 1.34 - 1.46: 2300 1.46 - 1.58: 4118 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9535 Sorted by residual: bond pdb=" N ASP A 323 " pdb=" CA ASP A 323 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.42e-02 4.96e+03 5.15e+00 bond pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 1.473 1.441 0.032 1.40e-02 5.10e+03 5.08e+00 bond pdb=" N PRO A 326 " pdb=" CD PRO A 326 " ideal model delta sigma weight residual 1.473 1.444 0.029 1.40e-02 5.10e+03 4.39e+00 bond pdb=" N GLU A 322 " pdb=" CA GLU A 322 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.25e-02 6.40e+03 4.31e+00 bond pdb=" CA THR A 320 " pdb=" C THR A 320 " ideal model delta sigma weight residual 1.528 1.505 0.023 1.13e-02 7.83e+03 4.21e+00 ... (remaining 9530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 12692 1.68 - 3.37: 194 3.37 - 5.05: 32 5.05 - 6.73: 5 6.73 - 8.42: 5 Bond angle restraints: 12928 Sorted by residual: angle pdb=" N VAL A 217 " pdb=" CA VAL A 217 " pdb=" C VAL A 217 " ideal model delta sigma weight residual 113.53 109.93 3.60 9.80e-01 1.04e+00 1.35e+01 angle pdb=" N PRO A 326 " pdb=" CD PRO A 326 " pdb=" CG PRO A 326 " ideal model delta sigma weight residual 103.20 97.72 5.48 1.50e+00 4.44e-01 1.34e+01 angle pdb=" CA THR A 319 " pdb=" CB THR A 319 " pdb=" OG1 THR A 319 " ideal model delta sigma weight residual 109.60 104.64 4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" CA THR A 320 " pdb=" CB THR A 320 " pdb=" OG1 THR A 320 " ideal model delta sigma weight residual 109.60 104.68 4.92 1.50e+00 4.44e-01 1.07e+01 angle pdb=" CA THR A 325 " pdb=" CB THR A 325 " pdb=" OG1 THR A 325 " ideal model delta sigma weight residual 109.60 104.70 4.90 1.50e+00 4.44e-01 1.07e+01 ... (remaining 12923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4754 17.96 - 35.92: 651 35.92 - 53.88: 195 53.88 - 71.84: 41 71.84 - 89.80: 10 Dihedral angle restraints: 5651 sinusoidal: 2236 harmonic: 3415 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 8.88 84.12 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -165.10 79.10 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual 93.00 144.63 -51.63 1 1.00e+01 1.00e-02 3.64e+01 ... (remaining 5648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1290 0.067 - 0.134: 136 0.134 - 0.201: 3 0.201 - 0.268: 0 0.268 - 0.335: 1 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CG LEU R 388 " pdb=" CB LEU R 388 " pdb=" CD1 LEU R 388 " pdb=" CD2 LEU R 388 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA TRP R 120 " pdb=" N TRP R 120 " pdb=" C TRP R 120 " pdb=" CB TRP R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CB ILE R 147 " pdb=" CA ILE R 147 " pdb=" CG1 ILE R 147 " pdb=" CG2 ILE R 147 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1427 not shown) Planarity restraints: 1647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 39 " 0.009 2.00e-02 2.50e+03 1.25e-02 3.89e+00 pdb=" CG TRP R 39 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP R 39 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP R 39 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 39 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 39 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 39 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 39 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO B 236 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 327 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO A 328 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 328 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 328 " 0.023 5.00e-02 4.00e+02 ... (remaining 1644 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 225 2.68 - 3.24: 8732 3.24 - 3.79: 14758 3.79 - 4.35: 19579 4.35 - 4.90: 32992 Nonbonded interactions: 76286 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.160 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.239 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.255 3.120 ... (remaining 76281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.920 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9541 Z= 0.159 Angle : 0.556 8.418 12940 Z= 0.308 Chirality : 0.043 0.335 1430 Planarity : 0.003 0.044 1647 Dihedral : 18.207 89.801 3425 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.87 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 Details of bonding type rmsd hydrogen bonds : bond 0.14477 ( 452) hydrogen bonds : angle 6.70021 ( 1293) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.96195 ( 12) covalent geometry : bond 0.00320 ( 9535) covalent geometry : angle 0.55586 (12928) *********************** 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 : 1.136 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: 1.1534 time to fit residues: 277.0691 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 : 1.139 ------------------------------------------------------------------------------- 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 9541 Z= 0.180 Angle : 0.620 9.269 12940 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 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 452) hydrogen bonds : angle 4.65369 ( 1293) SS BOND : bond 0.00213 ( 6) SS BOND : angle 0.93258 ( 12) covalent geometry : bond 0.00408 ( 9535) covalent geometry : angle 0.61999 (12928) *********************** 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 : 0.999 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: 1.0402 time to fit residues: 247.6255 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 : 1.036 ------------------------------------------------------------------------------- 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: 3.9990 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: 6.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.116047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.071083 restraints weight = 16738.580| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.05 r_work: 0.2733 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9541 Z= 0.115 Angle : 0.585 8.643 12940 Z= 0.300 Chirality : 0.042 0.157 1430 Planarity : 0.004 0.038 1647 Dihedral : 4.570 49.513 1288 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.60 % Favored : 95.23 % Rotamer: Outliers : 5.07 % Allowed : 32.94 % 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: 0.96 (0.26), residues: 1152 helix: 2.11 (0.25), residues: 448 sheet: 0.52 (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 A 220 PHE 0.009 0.001 PHE A 212 TYR 0.018 0.001 TYR R 145 ARG 0.005 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 452) hydrogen bonds : angle 4.37480 ( 1293) SS BOND : bond 0.00288 ( 6) SS BOND : angle 0.78179 ( 12) covalent geometry : bond 0.00249 ( 9535) covalent geometry : angle 0.58477 (12928) *********************** 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 221 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8561 (t80) cc_final: 0.8197 (t80) REVERT: R 204 MET cc_start: 0.8537 (mmm) cc_final: 0.7896 (mmp) REVERT: R 303 MET cc_start: 0.8074 (tmm) cc_final: 0.7836 (tmm) REVERT: A 31 GLN cc_start: 0.8737 (tp40) cc_final: 0.8197 (tm130) REVERT: A 35 GLN cc_start: 0.8634 (tt0) cc_final: 0.8040 (tm-30) REVERT: A 204 THR cc_start: 0.8886 (p) cc_final: 0.8669 (p) REVERT: A 239 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8810 (p0) REVERT: B 226 GLU cc_start: 0.8934 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 268 ASN cc_start: 0.8896 (t0) cc_final: 0.8627 (t0) REVERT: G 18 GLN cc_start: 0.8127 (tp40) cc_final: 0.7424 (tp40) REVERT: G 20 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8833 (mttp) REVERT: G 29 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8340 (mmmm) REVERT: G 62 ARG cc_start: 0.5496 (OUTLIER) cc_final: 0.5158 (ptp-170) REVERT: N 38 ARG cc_start: 0.9170 (ptt180) cc_final: 0.8755 (ptt90) REVERT: N 46 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: N 73 ASP cc_start: 0.7861 (t0) cc_final: 0.7455 (t0) REVERT: N 82 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7755 (mm-40) REVERT: N 84 ASN cc_start: 0.7756 (m-40) cc_final: 0.7442 (m110) REVERT: N 114 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.8919 (p) outliers start: 51 outliers final: 22 residues processed: 206 average time/residue: 1.0379 time to fit residues: 230.4570 Evaluate side-chains 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 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 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 104 THR 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: 0.0270 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 70 optimal weight: 0.0040 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4650 ------------------------------------------------------------------------------- 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 N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.115619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.071313 restraints weight = 16595.029| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.03 r_work: 0.2736 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9541 Z= 0.113 Angle : 0.579 9.373 12940 Z= 0.295 Chirality : 0.041 0.149 1430 Planarity : 0.003 0.037 1647 Dihedral : 4.305 48.045 1286 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 4.88 % Allowed : 32.84 % Favored : 62.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.26), residues: 1152 helix: 2.04 (0.25), residues: 457 sheet: 0.51 (0.33), residues: 225 loop : -0.74 (0.30), residues: 470 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 0.022 0.001 TYR R 69 ARG 0.008 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 452) hydrogen bonds : angle 4.24102 ( 1293) SS BOND : bond 0.00175 ( 6) SS BOND : angle 0.79890 ( 12) covalent geometry : bond 0.00251 ( 9535) covalent geometry : angle 0.57850 (12928) *********************** 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 212 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 1.105 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: 0.8540 (t80) cc_final: 0.8240 (t80) REVERT: R 152 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8572 (m-10) REVERT: R 204 MET cc_start: 0.8523 (mmm) cc_final: 0.7869 (mmp) REVERT: R 303 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7820 (tmm) REVERT: R 320 ASN cc_start: 0.8833 (m-40) cc_final: 0.8427 (t0) REVERT: A 31 GLN cc_start: 0.8668 (tp40) cc_final: 0.8200 (tm130) REVERT: A 35 GLN cc_start: 0.8602 (tt0) cc_final: 0.7987 (tm-30) REVERT: A 204 THR cc_start: 0.8862 (p) cc_final: 0.8615 (p) REVERT: A 265 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8992 (ptm160) REVERT: B 9 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9123 (mm-40) REVERT: B 152 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8974 (mp) REVERT: B 214 ARG cc_start: 0.9101 (ttm-80) cc_final: 0.8751 (ptm-80) REVERT: B 226 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8003 (mt-10) REVERT: B 268 ASN cc_start: 0.8922 (t0) cc_final: 0.8658 (t0) REVERT: G 18 GLN cc_start: 0.8193 (tp40) cc_final: 0.7435 (tp40) REVERT: G 29 LYS cc_start: 0.8690 (mmpt) cc_final: 0.8341 (mmmm) REVERT: G 46 LYS cc_start: 0.9484 (mtmm) cc_final: 0.8913 (ptpp) REVERT: G 62 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.5026 (ptp-170) REVERT: N 38 ARG cc_start: 0.9155 (ptt180) cc_final: 0.8717 (ptt90) REVERT: N 46 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: N 73 ASP cc_start: 0.7993 (t0) cc_final: 0.7632 (t0) REVERT: N 82 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7561 (tm-30) REVERT: N 84 ASN cc_start: 0.7800 (m-40) cc_final: 0.7434 (m110) REVERT: N 87 LYS cc_start: 0.7647 (mtmt) cc_final: 0.7399 (mtmt) REVERT: N 114 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.8977 (p) outliers start: 49 outliers final: 24 residues processed: 201 average time/residue: 0.9953 time to fit residues: 216.2944 Evaluate side-chains 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 265 ILE Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 303 MET 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 9 GLN Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 258 ASP 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 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: 1.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 32 optimal weight: 0.2980 chunk 6 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 239 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.071699 restraints weight = 16450.645| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.93 r_work: 0.2739 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 9541 Z= 0.151 Angle : 0.609 13.036 12940 Z= 0.312 Chirality : 0.043 0.264 1430 Planarity : 0.004 0.043 1647 Dihedral : 4.074 48.588 1285 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 4.38 % Allowed : 33.83 % Favored : 61.79 % 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: 2.10 (0.25), residues: 459 sheet: 0.46 (0.33), residues: 227 loop : -0.73 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.006 0.001 HIS R 171 PHE 0.008 0.001 PHE R 280 TYR 0.019 0.001 TYR R 145 ARG 0.007 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 452) hydrogen bonds : angle 4.17774 ( 1293) SS BOND : bond 0.00265 ( 6) SS BOND : angle 3.02511 ( 12) covalent geometry : bond 0.00356 ( 9535) covalent geometry : angle 0.60177 (12928) *********************** 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 199 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8584 (t80) cc_final: 0.8220 (t80) REVERT: R 80 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6749 (t80) REVERT: R 204 MET cc_start: 0.8538 (mmm) cc_final: 0.7874 (mmp) REVERT: R 227 ARG cc_start: 0.8959 (tmm160) cc_final: 0.8735 (tmm160) REVERT: R 303 MET cc_start: 0.8101 (tmm) cc_final: 0.7869 (tmm) REVERT: R 320 ASN cc_start: 0.8856 (m-40) cc_final: 0.8454 (t0) REVERT: A 31 GLN cc_start: 0.8632 (tp40) cc_final: 0.8100 (tm130) REVERT: A 35 GLN cc_start: 0.8608 (tt0) cc_final: 0.7978 (tm-30) REVERT: A 204 THR cc_start: 0.8903 (p) cc_final: 0.8669 (p) REVERT: A 239 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8769 (p0) REVERT: A 265 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8989 (ptm160) REVERT: B 152 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8984 (mp) REVERT: B 226 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 268 ASN cc_start: 0.8910 (t0) cc_final: 0.8642 (t0) REVERT: B 301 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8643 (mmtt) REVERT: G 18 GLN cc_start: 0.8136 (tp40) cc_final: 0.7504 (tp40) REVERT: G 20 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8827 (mttp) REVERT: G 62 ARG cc_start: 0.5635 (OUTLIER) cc_final: 0.5140 (ptp-170) REVERT: N 46 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: N 73 ASP cc_start: 0.8125 (t0) cc_final: 0.7320 (t0) REVERT: N 82 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7775 (mm-40) REVERT: N 84 ASN cc_start: 0.7913 (m-40) cc_final: 0.7685 (m110) REVERT: N 87 LYS cc_start: 0.7670 (mtmt) cc_final: 0.7376 (mtmt) outliers start: 44 outliers final: 24 residues processed: 189 average time/residue: 1.0538 time to fit residues: 214.7273 Evaluate side-chains 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 R residue 282 VAL 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 33 ILE Chi-restraints excluded: chain B residue 152 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 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 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 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: 0.6980 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 B 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.067830 restraints weight = 16646.140| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.93 r_work: 0.2685 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9541 Z= 0.239 Angle : 0.657 8.365 12940 Z= 0.338 Chirality : 0.045 0.187 1430 Planarity : 0.004 0.042 1647 Dihedral : 4.273 51.081 1284 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 4.58 % Allowed : 33.43 % 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: 0.91 (0.26), residues: 1152 helix: 2.01 (0.25), residues: 458 sheet: 0.48 (0.34), residues: 228 loop : -0.76 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS R 171 PHE 0.010 0.001 PHE A 238 TYR 0.055 0.002 TYR R 69 ARG 0.008 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 452) hydrogen bonds : angle 4.33517 ( 1293) SS BOND : bond 0.00238 ( 6) SS BOND : angle 2.29560 ( 12) covalent geometry : bond 0.00553 ( 9535) covalent geometry : angle 0.65311 (12928) *********************** 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 201 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8596 (t80) cc_final: 0.8230 (t80) REVERT: P 23 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6994 (pp30) REVERT: R 80 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6893 (t80) REVERT: R 204 MET cc_start: 0.8598 (mmm) cc_final: 0.7973 (mmp) REVERT: R 320 ASN cc_start: 0.8875 (m-40) cc_final: 0.8480 (t0) REVERT: A 31 GLN cc_start: 0.8713 (tp40) cc_final: 0.8115 (tm130) REVERT: A 265 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.9041 (ptm160) REVERT: A 283 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8068 (ptm160) REVERT: A 392 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8668 (mt-10) REVERT: B 9 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.8993 (mm-40) REVERT: B 226 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8218 (mt-10) REVERT: B 262 MET cc_start: 0.8661 (tpp) cc_final: 0.8150 (mtp) REVERT: B 268 ASN cc_start: 0.9000 (t0) cc_final: 0.8750 (t0) REVERT: B 301 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8689 (mmtt) REVERT: G 29 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8393 (mmmt) REVERT: G 62 ARG cc_start: 0.5697 (OUTLIER) cc_final: 0.5224 (ptp-170) REVERT: N 38 ARG cc_start: 0.9015 (ptm160) cc_final: 0.8729 (ptm-80) REVERT: N 46 GLU cc_start: 0.8276 (tt0) cc_final: 0.7759 (pt0) REVERT: N 73 ASP cc_start: 0.8168 (t0) cc_final: 0.7368 (t0) REVERT: N 82 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7792 (mm-40) REVERT: N 87 LYS cc_start: 0.7680 (mtmt) cc_final: 0.7395 (mtmt) REVERT: N 114 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9016 (p) outliers start: 46 outliers final: 26 residues processed: 193 average time/residue: 1.1139 time to fit residues: 230.6925 Evaluate side-chains 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 30 LEU 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 A residue 330 GLU Chi-restraints excluded: chain B residue 9 GLN 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 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 17 GLU 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 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: 0.7980 chunk 45 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 88 optimal weight: 0.0670 chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 23 GLN A 264 ASN B 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.113966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.070133 restraints weight = 16715.616| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.96 r_work: 0.2732 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9541 Z= 0.132 Angle : 0.640 11.314 12940 Z= 0.329 Chirality : 0.042 0.168 1430 Planarity : 0.004 0.053 1647 Dihedral : 4.372 49.726 1284 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % Rotamer: Outliers : 4.68 % Allowed : 33.83 % Favored : 61.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: 0.91 (0.26), residues: 1152 helix: 2.10 (0.25), residues: 458 sheet: 0.43 (0.33), residues: 228 loop : -0.82 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS R 171 PHE 0.009 0.001 PHE R 367 TYR 0.023 0.001 TYR R 69 ARG 0.015 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 452) hydrogen bonds : angle 4.21943 ( 1293) SS BOND : bond 0.00734 ( 6) SS BOND : angle 3.28900 ( 12) covalent geometry : bond 0.00311 ( 9535) covalent geometry : angle 0.63195 (12928) *********************** 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 206 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8574 (t80) cc_final: 0.8282 (t80) REVERT: R 71 CYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8202 (m) REVERT: R 80 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6848 (t80) REVERT: R 127 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: R 204 MET cc_start: 0.8593 (mmm) cc_final: 0.7963 (mmp) REVERT: R 320 ASN cc_start: 0.8873 (m-40) cc_final: 0.8505 (t0) REVERT: A 31 GLN cc_start: 0.8672 (tp40) cc_final: 0.8206 (tm130) REVERT: A 35 GLN cc_start: 0.8566 (tt0) cc_final: 0.7899 (tm-30) REVERT: A 239 ASN cc_start: 0.9193 (OUTLIER) cc_final: 0.8823 (p0) REVERT: A 265 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.9000 (ptm160) REVERT: A 392 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8682 (mt-10) REVERT: B 9 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.8983 (mm-40) REVERT: B 258 ASP cc_start: 0.8639 (t0) cc_final: 0.8416 (t0) REVERT: B 262 MET cc_start: 0.8624 (tpp) cc_final: 0.8196 (mtp) REVERT: B 268 ASN cc_start: 0.9008 (t0) cc_final: 0.8765 (t0) REVERT: B 301 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8637 (mmtt) REVERT: G 20 LYS cc_start: 0.9033 (ttmm) cc_final: 0.8754 (mtmp) REVERT: G 62 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.5477 (ptp-170) REVERT: N 73 ASP cc_start: 0.8137 (t0) cc_final: 0.7313 (t0) REVERT: N 82 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7639 (tm-30) REVERT: N 84 ASN cc_start: 0.7912 (m-40) cc_final: 0.7607 (m110) REVERT: N 87 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7442 (mtmt) REVERT: N 114 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9065 (p) outliers start: 47 outliers final: 24 residues processed: 199 average time/residue: 1.0290 time to fit residues: 221.3824 Evaluate side-chains 186 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain R residue 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 127 GLU 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 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 9 GLN 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 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** R 45 GLN A 264 ASN B 9 GLN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.070805 restraints weight = 16811.293| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.95 r_work: 0.2741 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9541 Z= 0.140 Angle : 0.660 12.893 12940 Z= 0.339 Chirality : 0.043 0.175 1430 Planarity : 0.004 0.048 1647 Dihedral : 4.344 49.043 1284 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 3.58 % Allowed : 34.83 % 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: 0.87 (0.26), residues: 1152 helix: 2.05 (0.25), residues: 459 sheet: 0.40 (0.33), residues: 228 loop : -0.84 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.008 0.001 HIS R 171 PHE 0.009 0.001 PHE R 367 TYR 0.022 0.001 TYR R 148 ARG 0.013 0.001 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 452) hydrogen bonds : angle 4.19342 ( 1293) SS BOND : bond 0.00348 ( 6) SS BOND : angle 2.92197 ( 12) covalent geometry : bond 0.00328 ( 9535) covalent geometry : angle 0.65452 (12928) *********************** 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 193 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8623 (t80) cc_final: 0.8325 (t80) REVERT: R 71 CYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8219 (m) REVERT: R 204 MET cc_start: 0.8587 (mmm) cc_final: 0.7958 (mmp) REVERT: R 320 ASN cc_start: 0.8881 (m-40) cc_final: 0.8519 (t0) REVERT: A 31 GLN cc_start: 0.8665 (tp40) cc_final: 0.8094 (tm130) REVERT: A 265 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8997 (ptm160) REVERT: A 283 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7958 (ptm160) REVERT: A 392 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8687 (mt-10) REVERT: B 9 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.8969 (mm-40) REVERT: B 226 GLU cc_start: 0.8801 (mt-10) cc_final: 0.7703 (mt-10) REVERT: B 262 MET cc_start: 0.8599 (tpp) cc_final: 0.8185 (mtp) REVERT: B 268 ASN cc_start: 0.9012 (t0) cc_final: 0.8786 (t0) REVERT: B 301 LYS cc_start: 0.9020 (mtpp) cc_final: 0.8642 (mmtt) REVERT: G 20 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8781 (mttp) REVERT: G 46 LYS cc_start: 0.9493 (mtmm) cc_final: 0.8936 (ptpp) REVERT: G 62 ARG cc_start: 0.5853 (OUTLIER) cc_final: 0.5508 (ptp-170) REVERT: N 45 LEU cc_start: 0.9107 (mt) cc_final: 0.8888 (mt) REVERT: N 46 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8035 (pt0) REVERT: N 73 ASP cc_start: 0.8177 (t0) cc_final: 0.7313 (t0) REVERT: N 76 LYS cc_start: 0.9471 (mtpm) cc_final: 0.9208 (mtpp) REVERT: N 82 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7627 (tm-30) REVERT: N 84 ASN cc_start: 0.7897 (m-40) cc_final: 0.7592 (m110) REVERT: N 87 LYS cc_start: 0.7680 (mtmt) cc_final: 0.7463 (mtmt) REVERT: N 114 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.9080 (p) outliers start: 36 outliers final: 21 residues processed: 185 average time/residue: 1.1407 time to fit residues: 227.2059 Evaluate side-chains 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 71 CYS Chi-restraints excluded: chain R residue 80 PHE 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 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 9 GLN 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 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: 2.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 9 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.113151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.069324 restraints weight = 16803.576| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.96 r_work: 0.2715 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9541 Z= 0.181 Angle : 0.677 11.743 12940 Z= 0.351 Chirality : 0.044 0.184 1430 Planarity : 0.004 0.048 1647 Dihedral : 4.376 50.121 1284 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 3.78 % Allowed : 35.12 % Favored : 61.09 % 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: 2.01 (0.25), residues: 458 sheet: 0.47 (0.33), residues: 225 loop : -0.94 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.010 0.001 HIS R 171 PHE 0.009 0.001 PHE B 151 TYR 0.023 0.002 TYR R 145 ARG 0.025 0.001 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 452) hydrogen bonds : angle 4.26026 ( 1293) SS BOND : bond 0.00311 ( 6) SS BOND : angle 2.82823 ( 12) covalent geometry : bond 0.00424 ( 9535) covalent geometry : angle 0.67184 (12928) *********************** 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 191 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8620 (t80) cc_final: 0.8315 (t80) REVERT: R 204 MET cc_start: 0.8594 (mmm) cc_final: 0.7972 (mmp) REVERT: R 303 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7294 (tpt) REVERT: R 320 ASN cc_start: 0.8833 (m-40) cc_final: 0.8506 (t0) REVERT: A 31 GLN cc_start: 0.8689 (tp40) cc_final: 0.8104 (tm130) REVERT: A 265 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.9031 (ptm160) REVERT: A 283 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8013 (ptm160) REVERT: A 392 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8697 (mt-10) REVERT: B 9 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8957 (mm-40) REVERT: B 226 GLU cc_start: 0.8815 (mt-10) cc_final: 0.7634 (mt-10) REVERT: B 262 MET cc_start: 0.8664 (tpp) cc_final: 0.8200 (mtp) REVERT: B 268 ASN cc_start: 0.9030 (t0) cc_final: 0.8804 (t0) REVERT: B 301 LYS cc_start: 0.9020 (mtpp) cc_final: 0.8643 (mmtt) REVERT: G 20 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8805 (mttp) REVERT: G 62 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5522 (ptp-170) REVERT: N 45 LEU cc_start: 0.9089 (mt) cc_final: 0.8866 (mt) REVERT: N 46 GLU cc_start: 0.8289 (tt0) cc_final: 0.8007 (pt0) REVERT: N 73 ASP cc_start: 0.8169 (t0) cc_final: 0.7309 (t0) REVERT: N 76 LYS cc_start: 0.9468 (mtpm) cc_final: 0.9208 (mtpp) REVERT: N 82 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7749 (mm-40) REVERT: N 87 LYS cc_start: 0.7643 (mtmt) cc_final: 0.7416 (mtmt) REVERT: N 114 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9093 (p) outliers start: 38 outliers final: 22 residues processed: 182 average time/residue: 1.1006 time to fit residues: 215.3265 Evaluate side-chains 182 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 80 PHE 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 303 MET Chi-restraints excluded: chain R residue 413 PHE 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 9 GLN 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 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 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: 0.6980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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** R 171 HIS A 264 ASN B 9 GLN G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.070676 restraints weight = 16878.215| |-----------------------------------------------------------------------------| r_work (start): 0.2907 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: 0.7829 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9541 Z= 0.140 Angle : 0.706 11.597 12940 Z= 0.360 Chirality : 0.044 0.202 1430 Planarity : 0.004 0.078 1647 Dihedral : 4.370 49.371 1284 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 2.89 % Allowed : 35.72 % Favored : 61.39 % 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: 2.02 (0.25), residues: 459 sheet: 0.41 (0.33), residues: 228 loop : -0.92 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 120 HIS 0.007 0.001 HIS R 171 PHE 0.011 0.001 PHE R 367 TYR 0.022 0.001 TYR P 19 ARG 0.030 0.001 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 452) hydrogen bonds : angle 4.20163 ( 1293) SS BOND : bond 0.00278 ( 6) SS BOND : angle 2.58895 ( 12) covalent geometry : bond 0.00332 ( 9535) covalent geometry : angle 0.70157 (12928) ********************** 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 187 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8625 (t80) cc_final: 0.8308 (t80) REVERT: R 204 MET cc_start: 0.8590 (mmm) cc_final: 0.7969 (mmp) REVERT: R 320 ASN cc_start: 0.8836 (m-40) cc_final: 0.8472 (t0) REVERT: A 31 GLN cc_start: 0.8674 (tp40) cc_final: 0.8205 (tm130) REVERT: A 239 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8845 (p0) REVERT: A 265 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.9015 (ptm160) REVERT: A 392 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8694 (mt-10) REVERT: B 20 ASP cc_start: 0.9241 (m-30) cc_final: 0.8904 (m-30) REVERT: B 215 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9015 (mm-30) REVERT: B 226 GLU cc_start: 0.8775 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 262 MET cc_start: 0.8624 (tpp) cc_final: 0.8222 (mtp) REVERT: B 268 ASN cc_start: 0.9034 (t0) cc_final: 0.8807 (t0) REVERT: B 301 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8694 (mmtt) REVERT: G 62 ARG cc_start: 0.5893 (OUTLIER) cc_final: 0.5565 (ptp-170) REVERT: N 38 ARG cc_start: 0.9021 (ptm160) cc_final: 0.8802 (ptm-80) REVERT: N 45 LEU cc_start: 0.9081 (mt) cc_final: 0.8820 (mt) REVERT: N 46 GLU cc_start: 0.8264 (tt0) cc_final: 0.7976 (pt0) REVERT: N 73 ASP cc_start: 0.8159 (t0) cc_final: 0.7323 (t0) REVERT: N 76 LYS cc_start: 0.9468 (mtpm) cc_final: 0.9211 (mtpp) REVERT: N 82 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: N 114 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9096 (p) outliers start: 29 outliers final: 22 residues processed: 183 average time/residue: 1.0994 time to fit residues: 216.0913 Evaluate side-chains 179 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR 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 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 9 GLN 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 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 82 GLN 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: 0.9980 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 9 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.071350 restraints weight = 16758.371| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.98 r_work: 0.2753 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9541 Z= 0.131 Angle : 0.694 11.524 12940 Z= 0.354 Chirality : 0.043 0.212 1430 Planarity : 0.004 0.066 1647 Dihedral : 4.326 48.643 1284 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 2.99 % Allowed : 36.32 % 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: 0.78 (0.26), residues: 1152 helix: 1.94 (0.25), residues: 465 sheet: 0.45 (0.34), residues: 225 loop : -0.95 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 120 HIS 0.003 0.000 HIS R 171 PHE 0.012 0.001 PHE R 367 TYR 0.023 0.001 TYR R 145 ARG 0.028 0.001 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 452) hydrogen bonds : angle 4.15808 ( 1293) SS BOND : bond 0.00250 ( 6) SS BOND : angle 2.22619 ( 12) covalent geometry : bond 0.00311 ( 9535) covalent geometry : angle 0.69127 (12928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6811.52 seconds wall clock time: 117 minutes 53.13 seconds (7073.13 seconds total)