Starting phenix.real_space_refine on Wed Jan 15 16:45:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw4_39622/01_2025/8yw4_39622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw4_39622/01_2025/8yw4_39622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw4_39622/01_2025/8yw4_39622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw4_39622/01_2025/8yw4_39622.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw4_39622/01_2025/8yw4_39622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw4_39622/01_2025/8yw4_39622.cif" } resolution = 3.26 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= 0.037 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 48 5.16 5 C 5466 2.51 5 N 1522 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8619 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2614 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2416 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 284} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 220 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'2ML:plan-1': 1, 'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.23, per 1000 atoms: 0.61 Number of scatterers: 8619 At special positions: 0 Unit cell: (84.609, 100.674, 162.792, 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 48 16.00 O 1583 8.00 N 1522 7.00 C 5466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " 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: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 43.7% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 removed outlier: 3.722A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.717A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.679A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.598A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.578A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.882A pdb=" N ASP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.577A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.662A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.875A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 48 removed outlier: 3.689A pdb=" N TYR R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG R 43 " --> pdb=" O TRP R 39 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU R 45 " --> pdb=" O ARG R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 161 removed outlier: 3.512A pdb=" N LEU R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 194 Processing helix chain 'R' and resid 196 through 201 removed outlier: 3.891A pdb=" N TYR R 200 " --> pdb=" O ARG R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 246 removed outlier: 3.501A pdb=" N LEU R 235 " --> pdb=" O TYR R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 265 Processing helix chain 'R' and resid 265 through 282 removed outlier: 3.674A pdb=" N LEU R 269 " --> pdb=" O GLY R 265 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 292 through 297 removed outlier: 3.537A pdb=" N TRP R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP R 297 " --> pdb=" O LYS R 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 292 through 297' Processing helix chain 'R' and resid 299 through 328 removed outlier: 3.677A pdb=" N ILE R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 351 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 358 removed outlier: 3.546A pdb=" N VAL R 356 " --> pdb=" O HIS R 353 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA R 358 " --> pdb=" O VAL R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 392 removed outlier: 3.886A pdb=" N PHE R 371 " --> pdb=" O GLY R 367 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE R 386 " --> pdb=" O SER R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 411 removed outlier: 3.947A pdb=" N ARG R 404 " --> pdb=" O GLN R 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 27 removed outlier: 3.513A pdb=" N ILE P 12 " --> pdb=" O SER P 8 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP P 15 " --> pdb=" O SER P 11 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS P 17 " --> pdb=" O 2ML P 13 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU P 24 " --> pdb=" O AIB P 20 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU P 27 " --> pdb=" O ILE P 23 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.860A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.613A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.503A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.548A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.248A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.788A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.679A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.629A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.992A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.687A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 423 hydrogen bonds defined for protein. 1194 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: 2.64 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2532 1.33 - 1.45: 1521 1.45 - 1.57: 4675 1.57 - 1.69: 1 1.69 - 1.81: 66 Bond restraints: 8795 Sorted by residual: bond pdb=" N GLY R 198 " pdb=" CA GLY R 198 " ideal model delta sigma weight residual 1.444 1.475 -0.031 8.80e-03 1.29e+04 1.24e+01 bond pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " ideal model delta sigma weight residual 1.525 1.578 -0.053 2.10e-02 2.27e+03 6.26e+00 bond pdb=" N ASP B 38 " pdb=" CA ASP B 38 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.45e-02 4.76e+03 6.13e+00 bond pdb=" N AIB P 20 " pdb=" CA AIB P 20 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.96e+00 bond pdb=" N AIB P 2 " pdb=" CA AIB P 2 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.60e+00 ... (remaining 8790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11721 1.89 - 3.79: 159 3.79 - 5.68: 21 5.68 - 7.58: 5 7.58 - 9.47: 3 Bond angle restraints: 11909 Sorted by residual: angle pdb=" O GLY R 198 " pdb=" C GLY R 198 " pdb=" N PRO R 199 " ideal model delta sigma weight residual 121.07 122.28 -1.21 3.60e-01 7.72e+00 1.13e+01 angle pdb=" N PHE A 282 " pdb=" CA PHE A 282 " pdb=" C PHE A 282 " ideal model delta sigma weight residual 114.56 110.45 4.11 1.27e+00 6.20e-01 1.05e+01 angle pdb=" N GLY R 198 " pdb=" CA GLY R 198 " pdb=" C GLY R 198 " ideal model delta sigma weight residual 115.22 111.58 3.64 1.27e+00 6.20e-01 8.21e+00 angle pdb=" CA LEU R 261 " pdb=" CB LEU R 261 " pdb=" CG LEU R 261 " ideal model delta sigma weight residual 116.30 125.77 -9.47 3.50e+00 8.16e-02 7.32e+00 angle pdb=" N PRO R 199 " pdb=" CA PRO R 199 " pdb=" C PRO R 199 " ideal model delta sigma weight residual 113.81 109.90 3.91 1.45e+00 4.76e-01 7.28e+00 ... (remaining 11904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4370 17.59 - 35.19: 600 35.19 - 52.78: 201 52.78 - 70.37: 40 70.37 - 87.97: 10 Dihedral angle restraints: 5221 sinusoidal: 2080 harmonic: 3141 Sorted by residual: dihedral pdb=" CB CYS R 216 " pdb=" SG CYS R 216 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 24.50 68.50 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 62.74 30.26 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA ASP R 129 " pdb=" CB ASP R 129 " pdb=" CG ASP R 129 " pdb=" OD1 ASP R 129 " ideal model delta sinusoidal sigma weight residual -30.00 -88.93 58.93 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 5218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1105 0.051 - 0.102: 181 0.102 - 0.153: 36 0.153 - 0.204: 0 0.204 - 0.255: 2 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " pdb=" CB1 2ML P 13 " pdb=" CB2 2ML P 13 " both_signs ideal model delta sigma weight residual False -2.84 -3.10 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU R 182 " pdb=" CB LEU R 182 " pdb=" CD1 LEU R 182 " pdb=" CD2 LEU R 182 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1321 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.039 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO G 60 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+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 ASP B 38 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 39 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.022 5.00e-02 4.00e+02 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 531 2.73 - 3.27: 8572 3.27 - 3.82: 14119 3.82 - 4.36: 16719 4.36 - 4.90: 29320 Nonbonded interactions: 69261 Sorted by model distance: nonbonded pdb=" NH2 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.190 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR R 225 " pdb=" O TRP R 264 " model vdw 2.249 3.040 ... (remaining 69256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.040 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 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 : 0.004 0.053 8795 Z= 0.262 Angle : 0.561 9.472 11909 Z= 0.296 Chirality : 0.040 0.255 1324 Planarity : 0.003 0.061 1518 Dihedral : 18.345 87.967 3189 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 0.33 % Allowed : 33.88 % Favored : 65.80 % 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: -0.25 (0.27), residues: 1054 helix: 1.23 (0.25), residues: 406 sheet: -1.13 (0.36), residues: 222 loop : -0.91 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.002 0.001 HIS B 183 PHE 0.024 0.001 PHE R 379 TYR 0.015 0.001 TYR R 335 ARG 0.004 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 212 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.6332 (mtp) cc_final: 0.6113 (ttm) REVERT: N 94 TYR cc_start: 0.6910 (m-80) cc_final: 0.5985 (m-80) REVERT: R 297 TRP cc_start: 0.7098 (m100) cc_final: 0.5925 (m-10) outliers start: 3 outliers final: 0 residues processed: 212 average time/residue: 0.2758 time to fit residues: 74.7100 Evaluate side-chains 132 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 0.0020 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 17 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 409 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.169576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122371 restraints weight = 10216.896| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.45 r_work: 0.3234 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8795 Z= 0.242 Angle : 0.644 11.033 11909 Z= 0.337 Chirality : 0.042 0.155 1324 Planarity : 0.005 0.042 1518 Dihedral : 4.037 36.374 1199 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.26 % Rotamer: Outliers : 5.75 % Allowed : 28.99 % Favored : 65.26 % 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: 0.42 (0.27), residues: 1054 helix: 2.01 (0.25), residues: 412 sheet: -1.15 (0.35), residues: 231 loop : -0.56 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.003 0.001 HIS R 242 PHE 0.014 0.002 PHE B 199 TYR 0.011 0.001 TYR P 25 ARG 0.006 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 157 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6854 (pt) REVERT: A 185 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: A 198 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.6972 (tmm) REVERT: B 13 GLN cc_start: 0.8249 (tp40) cc_final: 0.7989 (tm-30) REVERT: B 87 THR cc_start: 0.8215 (m) cc_final: 0.7968 (m) REVERT: B 226 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: B 262 MET cc_start: 0.7382 (mtp) cc_final: 0.7128 (ttm) REVERT: B 338 ILE cc_start: 0.7922 (mt) cc_final: 0.7481 (mt) REVERT: N 89 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: R 140 MET cc_start: 0.8212 (tmm) cc_final: 0.7924 (tmm) REVERT: R 297 TRP cc_start: 0.7424 (m100) cc_final: 0.6103 (m-10) outliers start: 53 outliers final: 19 residues processed: 192 average time/residue: 0.2140 time to fit residues: 56.6037 Evaluate side-chains 153 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 36 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 0.0270 chunk 20 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN R 175 ASN ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123562 restraints weight = 10299.205| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.46 r_work: 0.3281 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8795 Z= 0.200 Angle : 0.557 9.104 11909 Z= 0.294 Chirality : 0.041 0.216 1324 Planarity : 0.004 0.046 1518 Dihedral : 3.965 41.692 1199 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.84 % Favored : 94.97 % Rotamer: Outliers : 4.99 % Allowed : 28.88 % Favored : 66.12 % 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: 0.59 (0.27), residues: 1054 helix: 2.16 (0.25), residues: 409 sheet: -0.93 (0.35), residues: 231 loop : -0.55 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.002 0.001 HIS A 324 PHE 0.023 0.002 PHE A 343 TYR 0.015 0.001 TYR N 32 ARG 0.006 0.001 ARG R 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8012 (tp40) cc_final: 0.7299 (tp-100) REVERT: A 198 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7448 (tmm) REVERT: A 345 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8107 (t0) REVERT: B 87 THR cc_start: 0.8375 (m) cc_final: 0.8123 (m) REVERT: B 338 ILE cc_start: 0.8262 (mt) cc_final: 0.7832 (mt) REVERT: R 164 ARG cc_start: 0.5122 (mtt180) cc_final: 0.4410 (mmt180) REVERT: R 321 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7501 (tt) outliers start: 46 outliers final: 27 residues processed: 183 average time/residue: 0.2414 time to fit residues: 58.6537 Evaluate side-chains 167 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123460 restraints weight = 10327.663| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.34 r_work: 0.3267 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8795 Z= 0.231 Angle : 0.579 10.621 11909 Z= 0.298 Chirality : 0.042 0.225 1324 Planarity : 0.004 0.036 1518 Dihedral : 4.052 40.402 1199 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.12 % Favored : 94.69 % Rotamer: Outliers : 5.32 % Allowed : 27.80 % Favored : 66.88 % 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: 0.73 (0.27), residues: 1054 helix: 2.31 (0.25), residues: 409 sheet: -0.88 (0.35), residues: 228 loop : -0.49 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 233 HIS 0.004 0.001 HIS B 54 PHE 0.019 0.002 PHE N 68 TYR 0.011 0.001 TYR A 306 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7900 (tmm) REVERT: A 344 ASN cc_start: 0.8453 (t0) cc_final: 0.8102 (t0) REVERT: A 345 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8375 (t0) REVERT: B 17 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7393 (tt0) REVERT: B 87 THR cc_start: 0.8588 (m) cc_final: 0.8335 (m) REVERT: B 155 ASN cc_start: 0.8123 (t0) cc_final: 0.7630 (t0) REVERT: B 338 ILE cc_start: 0.8462 (mt) cc_final: 0.8025 (mt) REVERT: N 89 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: N 105 ARG cc_start: 0.8090 (mpp80) cc_final: 0.7688 (mpp80) REVERT: R 140 MET cc_start: 0.8472 (tmm) cc_final: 0.8007 (tmm) REVERT: R 164 ARG cc_start: 0.5258 (mtt180) cc_final: 0.4500 (mmt180) REVERT: R 297 TRP cc_start: 0.7553 (m100) cc_final: 0.6108 (m-10) outliers start: 49 outliers final: 34 residues processed: 188 average time/residue: 0.2422 time to fit residues: 60.9724 Evaluate side-chains 171 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 chunk 16 optimal weight: 7.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN R 173 HIS ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114405 restraints weight = 10350.182| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.70 r_work: 0.3123 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8795 Z= 0.292 Angle : 0.615 9.185 11909 Z= 0.318 Chirality : 0.043 0.213 1324 Planarity : 0.004 0.040 1518 Dihedral : 4.274 36.965 1199 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 5.86 % Allowed : 28.88 % Favored : 65.26 % 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: 0.54 (0.27), residues: 1054 helix: 2.11 (0.25), residues: 411 sheet: -0.92 (0.35), residues: 220 loop : -0.62 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 287 HIS 0.005 0.001 HIS B 54 PHE 0.027 0.002 PHE A 185 TYR 0.013 0.002 TYR A 306 ARG 0.005 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8423 (tpp) REVERT: A 310 ASP cc_start: 0.8691 (t0) cc_final: 0.8341 (m-30) REVERT: A 344 ASN cc_start: 0.8519 (t0) cc_final: 0.8080 (m-40) REVERT: A 345 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8476 (t70) REVERT: B 17 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7774 (tt0) REVERT: B 87 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8740 (m) REVERT: B 172 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 266 HIS cc_start: 0.7665 (OUTLIER) cc_final: 0.7425 (t-90) REVERT: B 267 ASP cc_start: 0.8596 (m-30) cc_final: 0.8115 (p0) REVERT: G 18 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7658 (tp40) REVERT: N 105 ARG cc_start: 0.8340 (mpp80) cc_final: 0.7952 (ptp-170) REVERT: R 164 ARG cc_start: 0.5514 (mtt180) cc_final: 0.4669 (mmt180) REVERT: R 182 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7756 (tt) REVERT: R 190 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.5893 (ttp-170) REVERT: R 297 TRP cc_start: 0.7801 (m100) cc_final: 0.6250 (m-10) outliers start: 54 outliers final: 32 residues processed: 207 average time/residue: 0.2320 time to fit residues: 64.6107 Evaluate side-chains 193 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 92 optimal weight: 0.0020 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS R 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.165324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117079 restraints weight = 10246.324| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.66 r_work: 0.3163 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.7195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8795 Z= 0.167 Angle : 0.533 11.772 11909 Z= 0.277 Chirality : 0.040 0.195 1324 Planarity : 0.003 0.037 1518 Dihedral : 3.994 36.125 1199 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.93 % Favored : 94.88 % Rotamer: Outliers : 4.56 % Allowed : 29.86 % Favored : 65.58 % 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: 0.62 (0.27), residues: 1054 helix: 2.22 (0.26), residues: 415 sheet: -0.78 (0.36), residues: 219 loop : -0.74 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 287 HIS 0.003 0.001 HIS B 54 PHE 0.014 0.001 PHE A 185 TYR 0.012 0.001 TYR R 141 ARG 0.004 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 310 ASP cc_start: 0.8602 (t0) cc_final: 0.8222 (m-30) REVERT: A 344 ASN cc_start: 0.8531 (t0) cc_final: 0.8086 (m-40) REVERT: A 345 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8415 (t70) REVERT: B 17 GLN cc_start: 0.8262 (tp-100) cc_final: 0.8019 (tt0) REVERT: B 87 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8725 (m) REVERT: B 172 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 267 ASP cc_start: 0.8640 (m-30) cc_final: 0.8072 (p0) REVERT: G 18 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7587 (tp40) REVERT: N 53 GLN cc_start: 0.7359 (mt0) cc_final: 0.7109 (mp10) REVERT: N 105 ARG cc_start: 0.8277 (mpp80) cc_final: 0.8049 (ptp90) REVERT: R 164 ARG cc_start: 0.5531 (mtt180) cc_final: 0.4686 (mmt180) outliers start: 42 outliers final: 26 residues processed: 188 average time/residue: 0.2266 time to fit residues: 57.7728 Evaluate side-chains 180 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 173 HIS Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 0.0060 chunk 60 optimal weight: 0.0970 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS R 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.165096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113344 restraints weight = 10358.931| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.50 r_work: 0.3168 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.7331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8795 Z= 0.169 Angle : 0.531 11.349 11909 Z= 0.274 Chirality : 0.040 0.140 1324 Planarity : 0.003 0.037 1518 Dihedral : 3.931 38.051 1199 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.12 % Rotamer: Outliers : 3.26 % Allowed : 31.38 % Favored : 65.36 % 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: 0.64 (0.27), residues: 1054 helix: 2.26 (0.26), residues: 415 sheet: -0.76 (0.35), residues: 223 loop : -0.75 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.016 0.001 HIS R 173 PHE 0.020 0.001 PHE P 6 TYR 0.010 0.001 TYR N 60 ARG 0.004 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 310 ASP cc_start: 0.8697 (t0) cc_final: 0.8335 (m-30) REVERT: A 344 ASN cc_start: 0.8549 (t0) cc_final: 0.8100 (m-40) REVERT: A 345 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8540 (t70) REVERT: B 87 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8768 (m) REVERT: B 172 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 267 ASP cc_start: 0.8612 (m-30) cc_final: 0.8094 (p0) REVERT: G 18 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7728 (tp40) REVERT: N 105 ARG cc_start: 0.8281 (mpp80) cc_final: 0.7997 (ptp-170) REVERT: R 164 ARG cc_start: 0.5448 (mtt180) cc_final: 0.4705 (mmt180) outliers start: 30 outliers final: 23 residues processed: 173 average time/residue: 0.2168 time to fit residues: 51.1408 Evaluate side-chains 172 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 285 GLN Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS R 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.164714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112773 restraints weight = 10457.708| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.51 r_work: 0.3161 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8795 Z= 0.179 Angle : 0.534 11.040 11909 Z= 0.276 Chirality : 0.040 0.241 1324 Planarity : 0.003 0.038 1518 Dihedral : 3.904 37.223 1199 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.88 % Favored : 93.93 % Rotamer: Outliers : 3.80 % Allowed : 30.84 % Favored : 65.36 % 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: 0.66 (0.27), residues: 1054 helix: 2.30 (0.26), residues: 415 sheet: -0.75 (0.34), residues: 235 loop : -0.76 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.006 0.001 HIS B 54 PHE 0.020 0.001 PHE A 185 TYR 0.010 0.001 TYR N 60 ARG 0.003 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 272 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8831 (tppt) REVERT: A 310 ASP cc_start: 0.8689 (t0) cc_final: 0.8336 (m-30) REVERT: A 344 ASN cc_start: 0.8504 (t0) cc_final: 0.8062 (m-40) REVERT: A 345 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8546 (t70) REVERT: B 87 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8794 (m) REVERT: B 172 GLU cc_start: 0.8229 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 267 ASP cc_start: 0.8626 (m-30) cc_final: 0.8110 (p0) REVERT: G 18 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7796 (tp40) REVERT: N 105 ARG cc_start: 0.8259 (mpp80) cc_final: 0.7985 (ptp-170) REVERT: R 147 LEU cc_start: 0.8481 (tp) cc_final: 0.8151 (tt) REVERT: R 164 ARG cc_start: 0.5610 (mtt180) cc_final: 0.4934 (mmt180) REVERT: R 190 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6112 (ttp-170) outliers start: 35 outliers final: 27 residues processed: 179 average time/residue: 0.2250 time to fit residues: 54.7984 Evaluate side-chains 182 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 0.0020 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.166184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124611 restraints weight = 9935.860| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.92 r_work: 0.3073 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.7790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8795 Z= 0.183 Angle : 0.541 11.459 11909 Z= 0.279 Chirality : 0.040 0.242 1324 Planarity : 0.003 0.038 1518 Dihedral : 3.876 34.336 1199 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 3.80 % Allowed : 31.16 % Favored : 65.04 % 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: 0.72 (0.27), residues: 1054 helix: 2.37 (0.26), residues: 418 sheet: -0.75 (0.35), residues: 234 loop : -0.76 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.025 0.001 PHE P 6 TYR 0.010 0.001 TYR N 60 ARG 0.003 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 272 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8863 (tppt) REVERT: A 310 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: A 344 ASN cc_start: 0.8543 (t0) cc_final: 0.8014 (m-40) REVERT: A 345 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8567 (t70) REVERT: B 87 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8851 (m) REVERT: G 18 GLN cc_start: 0.8398 (tp-100) cc_final: 0.8138 (tp40) REVERT: R 164 ARG cc_start: 0.5535 (mtt180) cc_final: 0.4921 (mmt180) REVERT: R 190 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6210 (ttp-170) REVERT: R 290 ASN cc_start: 0.7297 (m-40) cc_final: 0.6980 (m110) outliers start: 35 outliers final: 26 residues processed: 192 average time/residue: 0.2189 time to fit residues: 56.9582 Evaluate side-chains 187 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.161757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119951 restraints weight = 9870.741| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.89 r_work: 0.3021 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.8229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8795 Z= 0.302 Angle : 0.604 14.924 11909 Z= 0.311 Chirality : 0.042 0.250 1324 Planarity : 0.004 0.042 1518 Dihedral : 4.115 32.136 1199 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.41 % Favored : 94.40 % Rotamer: Outliers : 4.13 % Allowed : 31.05 % Favored : 64.82 % 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: 0.62 (0.27), residues: 1054 helix: 2.29 (0.26), residues: 419 sheet: -0.93 (0.34), residues: 231 loop : -0.72 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 287 HIS 0.004 0.001 HIS B 54 PHE 0.022 0.002 PHE A 185 TYR 0.020 0.002 TYR R 281 ARG 0.006 0.000 ARG N 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 272 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8861 (tppt) REVERT: A 310 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8439 (m-30) REVERT: A 344 ASN cc_start: 0.8637 (t0) cc_final: 0.8245 (m-40) REVERT: A 345 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8634 (t70) REVERT: B 33 ILE cc_start: 0.8675 (mm) cc_final: 0.8472 (mt) REVERT: B 35 ASN cc_start: 0.7714 (p0) cc_final: 0.7362 (p0) REVERT: B 87 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9082 (m) REVERT: G 18 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8166 (tp-100) REVERT: G 62 ARG cc_start: 0.7560 (tpp-160) cc_final: 0.7252 (mmp80) REVERT: R 164 ARG cc_start: 0.5409 (mtt180) cc_final: 0.4810 (mmt180) REVERT: R 190 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6353 (ttp-170) REVERT: R 290 ASN cc_start: 0.7373 (m-40) cc_final: 0.7060 (m110) REVERT: R 379 PHE cc_start: 0.8414 (t80) cc_final: 0.8163 (t80) outliers start: 38 outliers final: 31 residues processed: 203 average time/residue: 0.2124 time to fit residues: 59.1311 Evaluate side-chains 199 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.162808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121641 restraints weight = 10027.299| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.94 r_work: 0.3035 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.8381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8795 Z= 0.243 Angle : 0.575 13.158 11909 Z= 0.294 Chirality : 0.041 0.270 1324 Planarity : 0.003 0.040 1518 Dihedral : 4.038 31.745 1199 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 3.69 % Allowed : 32.03 % Favored : 64.28 % 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: 0.65 (0.27), residues: 1054 helix: 2.29 (0.26), residues: 419 sheet: -0.90 (0.34), residues: 231 loop : -0.69 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.020 0.001 PHE A 185 TYR 0.017 0.001 TYR R 281 ARG 0.003 0.000 ARG N 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4891.17 seconds wall clock time: 87 minutes 15.68 seconds (5235.68 seconds total)