Starting phenix.real_space_refine on Sun Jun 8 06:23:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivg_60927/06_2025/9ivg_60927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivg_60927/06_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_60927/06_2025/9ivg_60927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivg_60927/06_2025/9ivg_60927.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivg_60927/06_2025/9ivg_60927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivg_60927/06_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-5710/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: 5.63, per 1000 atoms: 0.60 Number of scatterers: 9325 At special positions: 0 Unit cell: (80.325, 99.603, 169.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1727 8.00 N 1612 7.00 C 5930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 41.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 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: 2.55 Time building geometry restraints manager: 2.81 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.710 Find NCS groups from input model: 0.090 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- 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 : 0.996 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: 1.1886 time to fit residues: 284.6536 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 : 1.093 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.113468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.070996 restraints weight = 16455.765| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.90 r_work: 0.2691 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 9.268 12940 Z= 0.321 Chirality : 0.043 0.185 1430 Planarity : 0.004 0.045 1647 Dihedral : 5.538 52.162 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 4.65372 ( 1293) SS BOND : bond 0.00213 ( 6) SS BOND : angle 0.93265 ( 12) covalent geometry : bond 0.00408 ( 9535) covalent geometry : angle 0.62000 (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 : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8563 (t80) cc_final: 0.8174 (t80) REVERT: R 204 MET cc_start: 0.8545 (mmm) cc_final: 0.7905 (mmp) REVERT: A 35 GLN cc_start: 0.8698 (tt0) cc_final: 0.8088 (tm-30) REVERT: B 10 GLU cc_start: 0.8875 (tp30) cc_final: 0.8645 (tp30) REVERT: B 197 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8376 (mmm-85) REVERT: B 226 GLU cc_start: 0.8944 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 260 GLU cc_start: 0.8675 (pt0) cc_final: 0.8144 (tt0) REVERT: B 262 MET cc_start: 0.8575 (mmm) cc_final: 0.8318 (tpp) REVERT: B 268 ASN cc_start: 0.8876 (t0) cc_final: 0.8601 (t0) REVERT: G 13 ARG cc_start: 0.8878 (ttp80) cc_final: 0.8669 (ttp80) REVERT: G 18 GLN cc_start: 0.8117 (tp40) cc_final: 0.7510 (tp40) REVERT: G 29 LYS cc_start: 0.8703 (mmpt) cc_final: 0.8409 (mmpt) REVERT: G 62 ARG cc_start: 0.5339 (OUTLIER) cc_final: 0.4889 (ptp-170) REVERT: N 38 ARG cc_start: 0.9139 (ptt180) cc_final: 0.8695 (ptt90) REVERT: N 46 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: N 73 ASP cc_start: 0.7753 (t0) cc_final: 0.7438 (t0) REVERT: N 82 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7719 (mm-40) REVERT: N 84 ASN cc_start: 0.7730 (m-40) cc_final: 0.7461 (m110) REVERT: N 114 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.8833 (p) outliers start: 53 outliers final: 21 residues processed: 221 average time/residue: 1.0639 time to fit residues: 253.0194 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 : 1.073 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 4 optimal weight: 40.0000 chunk 74 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.115404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.070286 restraints weight = 16758.723| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.06 r_work: 0.2719 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9541 Z= 0.124 Angle : 0.587 8.760 12940 Z= 0.301 Chirality : 0.042 0.156 1430 Planarity : 0.004 0.039 1647 Dihedral : 4.587 49.753 1288 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 4.98 % Allowed : 33.33 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1152 helix: 2.10 (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 0.012 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 R 64 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 452) hydrogen bonds : angle 4.37458 ( 1293) SS BOND : bond 0.00418 ( 6) SS BOND : angle 0.82658 ( 12) covalent geometry : bond 0.00276 ( 9535) covalent geometry : angle 0.58650 (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 217 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.018 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: 0.8208 (t80) REVERT: R 204 MET cc_start: 0.8540 (mmm) cc_final: 0.7904 (mmp) REVERT: R 303 MET cc_start: 0.8080 (tmm) cc_final: 0.7846 (tmm) REVERT: A 31 GLN cc_start: 0.8740 (tp40) cc_final: 0.8211 (tm130) REVERT: A 35 GLN cc_start: 0.8633 (tt0) cc_final: 0.8038 (tm-30) REVERT: A 204 THR cc_start: 0.8899 (p) cc_final: 0.8684 (p) REVERT: A 239 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8803 (p0) REVERT: B 197 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8222 (mmm-85) REVERT: B 214 ARG cc_start: 0.9151 (ttm-80) cc_final: 0.8617 (ptp-110) REVERT: B 226 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8000 (mt-10) REVERT: B 268 ASN cc_start: 0.8891 (t0) cc_final: 0.8618 (t0) REVERT: G 18 GLN cc_start: 0.8085 (tp40) cc_final: 0.7380 (tp40) REVERT: G 20 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8826 (mttp) REVERT: G 62 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.5186 (ptp-170) REVERT: N 38 ARG cc_start: 0.9165 (ptt180) cc_final: 0.8744 (ptt90) REVERT: N 46 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7703 (pt0) REVERT: N 73 ASP cc_start: 0.7874 (t0) cc_final: 0.7536 (t0) REVERT: N 82 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7684 (mm-40) REVERT: N 84 ASN cc_start: 0.7760 (m-40) cc_final: 0.7479 (m110) REVERT: N 114 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.8894 (p) outliers start: 50 outliers final: 24 residues processed: 203 average time/residue: 1.0817 time to fit residues: 236.1975 Evaluate side-chains 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 201 LEU 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 33 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 70 optimal weight: 0.0670 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 0.0570 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.114084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.071465 restraints weight = 16516.112| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.88 r_work: 0.2733 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9541 Z= 0.128 Angle : 0.577 8.914 12940 Z= 0.295 Chirality : 0.042 0.149 1430 Planarity : 0.003 0.038 1647 Dihedral : 4.358 49.138 1286 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 5.17 % Allowed : 32.74 % Favored : 62.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.26), residues: 1152 helix: 2.08 (0.25), residues: 458 sheet: 0.52 (0.33), residues: 226 loop : -0.71 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.008 0.001 PHE B 151 TYR 0.021 0.001 TYR R 69 ARG 0.008 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 452) hydrogen bonds : angle 4.23766 ( 1293) SS BOND : bond 0.00174 ( 6) SS BOND : angle 0.87933 ( 12) covalent geometry : bond 0.00289 ( 9535) covalent geometry : angle 0.57662 (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 208 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8552 (t80) cc_final: 0.8257 (t80) REVERT: R 80 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6875 (t80) REVERT: R 204 MET cc_start: 0.8557 (mmm) cc_final: 0.7903 (mmp) REVERT: R 303 MET cc_start: 0.8077 (tmm) cc_final: 0.7839 (tmm) REVERT: R 320 ASN cc_start: 0.8863 (m-40) cc_final: 0.8456 (t0) REVERT: A 31 GLN cc_start: 0.8687 (tp40) cc_final: 0.8217 (tm130) REVERT: A 35 GLN cc_start: 0.8618 (tt0) cc_final: 0.8001 (tm-30) REVERT: A 204 THR cc_start: 0.8905 (p) cc_final: 0.8677 (p) REVERT: A 265 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.9023 (ptm160) REVERT: B 172 GLU cc_start: 0.9109 (tt0) cc_final: 0.8721 (tp30) REVERT: B 197 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8407 (mmm-85) REVERT: B 215 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8687 (mp0) REVERT: B 226 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 268 ASN cc_start: 0.8937 (t0) cc_final: 0.8673 (t0) REVERT: G 18 GLN cc_start: 0.8219 (tp40) cc_final: 0.7457 (tp40) REVERT: G 29 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8430 (mmmt) REVERT: G 62 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.5015 (ptp-170) REVERT: N 38 ARG cc_start: 0.9197 (ptt180) cc_final: 0.8730 (ptt90) REVERT: N 46 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: N 73 ASP cc_start: 0.8063 (t0) cc_final: 0.7728 (t0) REVERT: N 82 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7614 (tm-30) REVERT: N 84 ASN cc_start: 0.7865 (m-40) cc_final: 0.7518 (m110) REVERT: N 114 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.8955 (p) outliers start: 52 outliers final: 25 residues processed: 197 average time/residue: 1.0682 time to fit residues: 226.5867 Evaluate side-chains 181 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 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 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 0.0070 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 78 optimal weight: 0.0570 chunk 74 optimal weight: 0.6980 chunk 32 optimal weight: 0.0060 chunk 6 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 overall best weight: 0.2932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 9 GLN B 239 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.072050 restraints weight = 16526.846| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.96 r_work: 0.2757 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9541 Z= 0.110 Angle : 0.574 9.809 12940 Z= 0.294 Chirality : 0.041 0.146 1430 Planarity : 0.004 0.049 1647 Dihedral : 4.239 48.072 1286 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 4.78 % Allowed : 33.33 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1152 helix: 2.12 (0.25), residues: 459 sheet: 0.51 (0.33), residues: 225 loop : -0.72 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.005 0.000 HIS R 171 PHE 0.009 0.001 PHE A 212 TYR 0.020 0.001 TYR R 145 ARG 0.007 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 452) hydrogen bonds : angle 4.13631 ( 1293) SS BOND : bond 0.00202 ( 6) SS BOND : angle 0.76412 ( 12) covalent geometry : bond 0.00243 ( 9535) covalent geometry : angle 0.57384 (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 213 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8568 (t80) cc_final: 0.8288 (t80) REVERT: R 80 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6775 (t80) REVERT: R 152 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8549 (m-10) REVERT: R 204 MET cc_start: 0.8542 (mmm) cc_final: 0.7891 (mmp) REVERT: R 320 ASN cc_start: 0.8830 (m-40) cc_final: 0.8434 (t0) REVERT: A 31 GLN cc_start: 0.8647 (tp40) cc_final: 0.8179 (tm130) REVERT: A 35 GLN cc_start: 0.8596 (tt0) cc_final: 0.7948 (tm-30) REVERT: A 204 THR cc_start: 0.8868 (p) cc_final: 0.8614 (p) REVERT: A 239 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8671 (p0) REVERT: A 265 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8953 (ptm160) REVERT: A 358 TYR cc_start: 0.8438 (m-80) cc_final: 0.8181 (m-80) REVERT: B 172 GLU cc_start: 0.9107 (tt0) cc_final: 0.8721 (tp30) REVERT: B 214 ARG cc_start: 0.9085 (ttm-80) cc_final: 0.8724 (ptm-80) REVERT: B 226 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8023 (mt-10) REVERT: B 268 ASN cc_start: 0.8916 (t0) cc_final: 0.8666 (t0) REVERT: B 301 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8678 (mmtt) REVERT: G 20 LYS cc_start: 0.9049 (ttmm) cc_final: 0.8785 (mtmp) REVERT: G 46 LYS cc_start: 0.9490 (mtmm) cc_final: 0.8963 (ptpp) REVERT: G 62 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.5234 (ptp-170) REVERT: N 28 THR cc_start: 0.8181 (m) cc_final: 0.7639 (p) REVERT: N 46 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: N 73 ASP cc_start: 0.8135 (t0) cc_final: 0.7301 (t0) REVERT: N 82 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7739 (tm-30) REVERT: N 84 ASN cc_start: 0.7898 (m-40) cc_final: 0.7552 (m110) REVERT: N 87 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7476 (mtmt) REVERT: N 114 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9053 (p) outliers start: 48 outliers final: 27 residues processed: 203 average time/residue: 1.0336 time to fit residues: 226.4911 Evaluate side-chains 189 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU 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 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 G 18 GLN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.069521 restraints weight = 16612.396| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.95 r_work: 0.2713 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9541 Z= 0.186 Angle : 0.635 10.737 12940 Z= 0.326 Chirality : 0.043 0.238 1430 Planarity : 0.004 0.036 1647 Dihedral : 4.086 49.548 1285 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 4.58 % Allowed : 33.73 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: 0.99 (0.26), residues: 1152 helix: 2.14 (0.25), residues: 458 sheet: 0.46 (0.33), residues: 228 loop : -0.76 (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 0.009 0.001 PHE A 238 TYR 0.058 0.002 TYR R 69 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 452) hydrogen bonds : angle 4.18542 ( 1293) SS BOND : bond 0.00251 ( 6) SS BOND : angle 2.90073 ( 12) covalent geometry : bond 0.00435 ( 9535) covalent geometry : angle 0.62931 (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 204 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8608 (t80) cc_final: 0.8259 (t80) REVERT: R 80 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6796 (t80) REVERT: R 152 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: R 204 MET cc_start: 0.8549 (mmm) cc_final: 0.7894 (mmp) REVERT: R 320 ASN cc_start: 0.8876 (m-40) cc_final: 0.8492 (t0) REVERT: A 31 GLN cc_start: 0.8676 (tp40) cc_final: 0.8091 (tm130) REVERT: A 35 GLN cc_start: 0.8594 (tt0) cc_final: 0.7940 (tm-30) REVERT: A 204 THR cc_start: 0.8961 (p) cc_final: 0.8748 (p) REVERT: A 265 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.9024 (ptm160) REVERT: A 283 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7992 (ptm160) REVERT: B 124 TYR cc_start: 0.8776 (m-80) cc_final: 0.8517 (m-80) REVERT: B 172 GLU cc_start: 0.9094 (tt0) cc_final: 0.8702 (tp30) REVERT: B 214 ARG cc_start: 0.9026 (ttm-80) cc_final: 0.8802 (ptm-80) REVERT: B 215 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8926 (tp30) REVERT: B 226 GLU cc_start: 0.9020 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 262 MET cc_start: 0.8582 (tpp) cc_final: 0.8137 (mtp) REVERT: B 268 ASN cc_start: 0.8976 (t0) cc_final: 0.8727 (t0) REVERT: B 301 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8677 (mmtt) REVERT: G 13 ARG cc_start: 0.8478 (ptp-110) cc_final: 0.8276 (ttp80) REVERT: G 62 ARG cc_start: 0.5610 (OUTLIER) cc_final: 0.5222 (ptp-170) REVERT: N 28 THR cc_start: 0.8351 (m) cc_final: 0.7852 (p) REVERT: N 38 ARG cc_start: 0.9066 (ptm160) cc_final: 0.8831 (ptm-80) REVERT: N 46 GLU cc_start: 0.8265 (tt0) cc_final: 0.7840 (pt0) REVERT: N 73 ASP cc_start: 0.8172 (t0) cc_final: 0.7335 (t0) REVERT: N 82 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7789 (mm-40) REVERT: N 87 LYS cc_start: 0.7671 (mtmt) cc_final: 0.7410 (mtmt) REVERT: N 98 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8327 (ttp-170) outliers start: 46 outliers final: 25 residues processed: 193 average time/residue: 1.1217 time to fit residues: 232.2756 Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain 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 70 ILE Chi-restraints excluded: chain N residue 98 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN G 18 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.070503 restraints weight = 16808.612| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.97 r_work: 0.2730 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9541 Z= 0.145 Angle : 0.625 10.130 12940 Z= 0.322 Chirality : 0.043 0.174 1430 Planarity : 0.004 0.046 1647 Dihedral : 4.080 49.003 1284 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 4.18 % Allowed : 34.23 % Favored : 61.59 % 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: 2.10 (0.25), residues: 459 sheet: 0.44 (0.33), residues: 228 loop : -0.79 (0.30), residues: 465 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 0.008 0.001 PHE B 151 TYR 0.026 0.001 TYR R 69 ARG 0.008 0.000 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 452) hydrogen bonds : angle 4.17613 ( 1293) SS BOND : bond 0.00276 ( 6) SS BOND : angle 2.43876 ( 12) covalent geometry : bond 0.00336 ( 9535) covalent geometry : angle 0.62073 (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 203 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8577 (t80) cc_final: 0.8227 (t80) REVERT: R 71 CYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8153 (m) REVERT: R 80 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6841 (t80) REVERT: R 127 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: R 152 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: R 204 MET cc_start: 0.8581 (mmm) cc_final: 0.7942 (mmp) REVERT: R 320 ASN cc_start: 0.8856 (m-40) cc_final: 0.8479 (t0) REVERT: A 31 GLN cc_start: 0.8699 (tp40) cc_final: 0.8104 (tm130) REVERT: A 35 GLN cc_start: 0.8542 (tt0) cc_final: 0.7886 (tm-30) REVERT: A 204 THR cc_start: 0.8961 (p) cc_final: 0.8744 (p) REVERT: A 265 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.9006 (ptm160) REVERT: A 283 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8031 (ptm160) REVERT: A 392 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8689 (mt-10) REVERT: B 124 TYR cc_start: 0.8782 (m-80) cc_final: 0.8510 (m-80) REVERT: B 172 GLU cc_start: 0.9086 (tt0) cc_final: 0.8698 (tp30) REVERT: B 215 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8727 (mp0) REVERT: B 262 MET cc_start: 0.8534 (tpp) cc_final: 0.8197 (mtp) REVERT: B 268 ASN cc_start: 0.9004 (t0) cc_final: 0.8747 (t0) REVERT: B 301 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8653 (mmtt) REVERT: G 46 LYS cc_start: 0.9481 (mtmm) cc_final: 0.8930 (ptpp) REVERT: G 62 ARG cc_start: 0.5718 (OUTLIER) cc_final: 0.5396 (ptp-170) REVERT: N 73 ASP cc_start: 0.8151 (t0) cc_final: 0.7326 (t0) REVERT: N 82 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7640 (tm-30) REVERT: N 84 ASN cc_start: 0.7904 (m-40) cc_final: 0.7594 (m110) REVERT: N 87 LYS cc_start: 0.7665 (mtmt) cc_final: 0.7440 (mtmt) REVERT: N 114 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9092 (p) outliers start: 42 outliers final: 23 residues processed: 194 average time/residue: 1.1384 time to fit residues: 237.3835 Evaluate side-chains 186 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 71 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 127 GLU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 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: 8.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 239 ASN G 18 GLN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.112536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.068569 restraints weight = 16957.015| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.98 r_work: 0.2693 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9541 Z= 0.206 Angle : 0.656 9.350 12940 Z= 0.337 Chirality : 0.044 0.156 1430 Planarity : 0.004 0.059 1647 Dihedral : 4.246 50.329 1284 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.56 % Favored : 94.27 % Rotamer: Outliers : 4.18 % Allowed : 34.33 % Favored : 61.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.26), residues: 1152 helix: 1.99 (0.25), residues: 464 sheet: 0.40 (0.33), residues: 229 loop : -0.71 (0.30), residues: 459 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 0.022 0.002 TYR R 145 ARG 0.012 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 452) hydrogen bonds : angle 4.28067 ( 1293) SS BOND : bond 0.00226 ( 6) SS BOND : angle 2.12774 ( 12) covalent geometry : bond 0.00479 ( 9535) covalent geometry : angle 0.65311 (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 200 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8579 (t80) cc_final: 0.8335 (t80) REVERT: R 71 CYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8152 (m) REVERT: R 80 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6872 (t80) REVERT: R 204 MET cc_start: 0.8616 (mmm) cc_final: 0.8004 (mmp) REVERT: R 303 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7296 (tpt) REVERT: R 320 ASN cc_start: 0.8853 (m-40) cc_final: 0.8516 (t0) REVERT: A 31 GLN cc_start: 0.8715 (tp40) cc_final: 0.8213 (tm130) REVERT: A 265 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.9025 (ptm160) REVERT: A 283 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8061 (ptm160) REVERT: A 392 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8677 (mt-10) REVERT: B 124 TYR cc_start: 0.8783 (m-80) cc_final: 0.8432 (m-80) REVERT: B 172 GLU cc_start: 0.9080 (tt0) cc_final: 0.8707 (tp30) REVERT: B 226 GLU cc_start: 0.8960 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 262 MET cc_start: 0.8610 (tpp) cc_final: 0.8152 (mtp) REVERT: B 268 ASN cc_start: 0.9016 (t0) cc_final: 0.8776 (t0) REVERT: B 301 LYS cc_start: 0.9020 (mtpp) cc_final: 0.8640 (mmtt) REVERT: G 62 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.5473 (ptp-170) REVERT: N 45 LEU cc_start: 0.9138 (mt) cc_final: 0.8905 (mt) REVERT: N 46 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: N 73 ASP cc_start: 0.8193 (t0) cc_final: 0.7369 (t0) REVERT: N 82 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7736 (mm-40) REVERT: N 87 LYS cc_start: 0.7672 (mtmt) cc_final: 0.7415 (mtmt) REVERT: N 106 ASP cc_start: 0.7634 (p0) cc_final: 0.7221 (p0) REVERT: N 114 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9082 (p) outliers start: 42 outliers final: 24 residues processed: 191 average time/residue: 1.1090 time to fit residues: 227.3638 Evaluate side-chains 183 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 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 18 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 chunk 12 optimal weight: 0.0170 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 0.0040 chunk 42 optimal weight: 0.9980 overall best weight: 0.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 88 ASN B 239 ASN G 18 GLN G 59 ASN N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.115236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.071364 restraints weight = 16665.900| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.05 r_work: 0.2747 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9541 Z= 0.122 Angle : 0.649 10.474 12940 Z= 0.329 Chirality : 0.042 0.160 1430 Planarity : 0.004 0.045 1647 Dihedral : 4.089 48.280 1284 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 2.09 % Allowed : 36.22 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1152 helix: 2.12 (0.25), residues: 459 sheet: 0.40 (0.33), residues: 227 loop : -0.85 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.006 0.001 HIS R 171 PHE 0.012 0.001 PHE R 367 TYR 0.020 0.001 TYR P 19 ARG 0.016 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 452) hydrogen bonds : angle 4.16056 ( 1293) SS BOND : bond 0.00215 ( 6) SS BOND : angle 1.84010 ( 12) covalent geometry : bond 0.00286 ( 9535) covalent geometry : angle 0.64647 (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 178 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8605 (t80) cc_final: 0.8292 (t80) REVERT: R 71 CYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8115 (m) REVERT: R 204 MET cc_start: 0.8582 (mmm) cc_final: 0.7953 (mmp) REVERT: R 320 ASN cc_start: 0.8858 (m-40) cc_final: 0.8525 (t0) REVERT: A 31 GLN cc_start: 0.8653 (tp40) cc_final: 0.8078 (tm130) REVERT: A 204 THR cc_start: 0.8958 (p) cc_final: 0.8703 (p) REVERT: A 265 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8961 (ptm160) REVERT: A 317 ARG cc_start: 0.9228 (mtm-85) cc_final: 0.8970 (ptp-110) REVERT: A 358 TYR cc_start: 0.8457 (m-80) cc_final: 0.8179 (m-80) REVERT: B 20 ASP cc_start: 0.9223 (m-30) cc_final: 0.8954 (p0) REVERT: B 45 MET cc_start: 0.9562 (mtt) cc_final: 0.9320 (mtt) REVERT: B 172 GLU cc_start: 0.9089 (tt0) cc_final: 0.8743 (tp30) REVERT: B 226 GLU cc_start: 0.8771 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 262 MET cc_start: 0.8518 (tpp) cc_final: 0.8186 (mtp) REVERT: B 268 ASN cc_start: 0.9025 (t0) cc_final: 0.8796 (t0) REVERT: B 301 LYS cc_start: 0.8994 (mtpp) cc_final: 0.8600 (mmtt) REVERT: G 46 LYS cc_start: 0.9471 (mtmm) cc_final: 0.8911 (ptpp) REVERT: G 62 ARG cc_start: 0.5804 (OUTLIER) cc_final: 0.5491 (ptp-170) REVERT: N 45 LEU cc_start: 0.9038 (mt) cc_final: 0.8779 (mt) REVERT: N 46 GLU cc_start: 0.8257 (tt0) cc_final: 0.7985 (pt0) REVERT: N 73 ASP cc_start: 0.8144 (t0) cc_final: 0.7313 (t0) REVERT: N 76 LYS cc_start: 0.9459 (mtpm) cc_final: 0.9204 (mtpp) REVERT: N 82 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7630 (tm-30) REVERT: N 84 ASN cc_start: 0.7870 (m-40) cc_final: 0.7588 (m110) REVERT: N 87 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7413 (mtmt) REVERT: N 114 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9080 (p) outliers start: 21 outliers final: 15 residues processed: 175 average time/residue: 1.1237 time to fit residues: 210.9824 Evaluate side-chains 174 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN G 59 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.071225 restraints weight = 16823.241| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.98 r_work: 0.2748 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9541 Z= 0.140 Angle : 0.688 11.423 12940 Z= 0.348 Chirality : 0.043 0.174 1430 Planarity : 0.004 0.056 1647 Dihedral : 4.251 49.112 1284 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 2.29 % Allowed : 36.52 % Favored : 61.19 % 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: 0.88 (0.26), residues: 1152 helix: 2.09 (0.25), residues: 459 sheet: 0.48 (0.34), residues: 225 loop : -0.90 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.000 HIS R 171 PHE 0.011 0.001 PHE R 367 TYR 0.023 0.001 TYR R 145 ARG 0.014 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 452) hydrogen bonds : angle 4.14300 ( 1293) SS BOND : bond 0.00349 ( 6) SS BOND : angle 3.28515 ( 12) covalent geometry : bond 0.00337 ( 9535) covalent geometry : angle 0.68095 (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 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 PHE cc_start: 0.8596 (t80) cc_final: 0.8269 (t80) REVERT: R 71 CYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8005 (m) REVERT: R 204 MET cc_start: 0.8587 (mmm) cc_final: 0.7956 (mmp) REVERT: R 320 ASN cc_start: 0.8883 (m-40) cc_final: 0.8539 (t0) REVERT: A 31 GLN cc_start: 0.8672 (tp40) cc_final: 0.8105 (tm130) REVERT: A 265 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8990 (ptm160) REVERT: A 317 ARG cc_start: 0.9220 (mtm-85) cc_final: 0.8959 (ptp-110) REVERT: A 392 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8695 (mt-10) REVERT: B 20 ASP cc_start: 0.9229 (m-30) cc_final: 0.8962 (p0) REVERT: B 172 GLU cc_start: 0.9087 (tt0) cc_final: 0.8759 (tp30) REVERT: B 215 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9073 (tp30) REVERT: B 226 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8179 (mt-10) REVERT: B 262 MET cc_start: 0.8539 (tpp) cc_final: 0.8179 (mtp) REVERT: B 268 ASN cc_start: 0.9017 (t0) cc_final: 0.8793 (t0) REVERT: G 29 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8348 (mmmt) REVERT: G 46 LYS cc_start: 0.9470 (mtmm) cc_final: 0.8910 (ptpp) REVERT: G 62 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5561 (ptp-170) REVERT: N 38 ARG cc_start: 0.9026 (ptm160) cc_final: 0.8809 (ptm-80) REVERT: N 45 LEU cc_start: 0.9079 (mt) cc_final: 0.8826 (mt) REVERT: N 46 GLU cc_start: 0.8299 (tt0) cc_final: 0.8021 (pt0) REVERT: N 73 ASP cc_start: 0.8155 (t0) cc_final: 0.7344 (t0) REVERT: N 82 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7619 (tm-30) REVERT: N 84 ASN cc_start: 0.7920 (m-40) cc_final: 0.7656 (m110) REVERT: N 87 LYS cc_start: 0.7644 (mtmt) cc_final: 0.7425 (mtmt) REVERT: N 114 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.9114 (p) outliers start: 23 outliers final: 16 residues processed: 180 average time/residue: 1.1507 time to fit residues: 222.2278 Evaluate side-chains 172 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 413 PHE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN G 59 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.071317 restraints weight = 16789.103| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.98 r_work: 0.2754 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 9541 Z= 0.136 Angle : 0.676 11.167 12940 Z= 0.342 Chirality : 0.043 0.188 1430 Planarity : 0.004 0.054 1647 Dihedral : 4.237 49.489 1284 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 2.39 % Allowed : 36.42 % Favored : 61.19 % 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: 0.83 (0.26), residues: 1152 helix: 2.02 (0.25), residues: 465 sheet: 0.44 (0.33), residues: 227 loop : -0.94 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 120 HIS 0.005 0.001 HIS R 171 PHE 0.012 0.001 PHE R 367 TYR 0.032 0.001 TYR R 88 ARG 0.014 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 452) hydrogen bonds : angle 4.16172 ( 1293) SS BOND : bond 0.00315 ( 6) SS BOND : angle 2.54776 ( 12) covalent geometry : bond 0.00327 ( 9535) covalent geometry : angle 0.67210 (12928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6862.15 seconds wall clock time: 117 minutes 56.47 seconds (7076.47 seconds total)