Starting phenix.real_space_refine on Fri Aug 22 20:43:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jr9_36593/08_2025/8jr9_36593_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jr9_36593/08_2025/8jr9_36593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jr9_36593/08_2025/8jr9_36593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jr9_36593/08_2025/8jr9_36593.map" model { file = "/net/cci-nas-00/data/ceres_data/8jr9_36593/08_2025/8jr9_36593_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jr9_36593/08_2025/8jr9_36593_neut_trim.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 5027 2.51 5 N 1346 2.21 5 O 1469 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "B ASP 186": not complete - not flipped Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7893 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1917 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2547 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 7, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 389 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2027 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 250} Chain breaks: 3 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'KHF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.25, per 1000 atoms: 0.29 Number of scatterers: 7893 At special positions: 0 Unit cell: (92.288, 108.768, 106.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 F 3 9.00 O 1469 8.00 N 1346 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.10 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: 0.74 Conformation dependent library (CDL) restraints added in 441.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 42.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 removed outlier: 4.007A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.558A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.833A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (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 35 removed outlier: 3.517A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.033A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 112 removed outlier: 4.495A pdb=" N THR N 111 " --> pdb=" O PHE N 108 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER N 112 " --> pdb=" O ASP N 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 108 through 112' Processing helix chain 'R' and resid 186 through 212 removed outlier: 3.566A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 243 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.624A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 Processing helix chain 'R' and resid 360 through 393 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 414 Processing helix chain 'R' and resid 415 through 427 removed outlier: 4.366A pdb=" N VAL R 419 " --> pdb=" O PRO R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 460 removed outlier: 4.914A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.441A pdb=" N VAL A 224 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY A 40 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 35 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A 245 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 37 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A 247 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A 39 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ASP A 249 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.611A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.524A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.778A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.657A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.706A 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: 3.825A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.639A 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 234 removed outlier: 6.878A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.582A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.577A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.929A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1286 1.30 - 1.43: 2203 1.43 - 1.56: 4509 1.56 - 1.68: 1 1.68 - 1.81: 65 Bond restraints: 8064 Sorted by residual: bond pdb=" C16 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 1.274 1.458 -0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" C25 KHF R 601 " pdb=" N4 KHF R 601 " ideal model delta sigma weight residual 1.353 1.455 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C12 KHF R 601 " pdb=" C13 KHF R 601 " ideal model delta sigma weight residual 1.530 1.429 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C13 KHF R 601 " pdb=" C14 KHF R 601 " ideal model delta sigma weight residual 1.532 1.440 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C TYR B 145 " pdb=" N LEU B 146 " ideal model delta sigma weight residual 1.331 1.275 0.055 1.41e-02 5.03e+03 1.54e+01 ... (remaining 8059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 10934 4.44 - 8.88: 21 8.88 - 13.32: 1 13.32 - 17.76: 1 17.76 - 22.20: 2 Bond angle restraints: 10959 Sorted by residual: angle pdb=" C12 KHF R 601 " pdb=" C13 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 110.89 133.09 -22.20 3.00e+00 1.11e-01 5.48e+01 angle pdb=" C14 KHF R 601 " pdb=" C13 KHF R 601 " pdb=" N2 KHF R 601 " ideal model delta sigma weight residual 110.23 90.48 19.75 3.00e+00 1.11e-01 4.33e+01 angle pdb=" O1 KHF R 601 " pdb=" S1 KHF R 601 " pdb=" O2 KHF R 601 " ideal model delta sigma weight residual 118.72 101.40 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O TYR B 145 " pdb=" C TYR B 145 " pdb=" N LEU B 146 " ideal model delta sigma weight residual 122.89 116.90 5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" N GLN A 294 " pdb=" CA GLN A 294 " pdb=" C GLN A 294 " ideal model delta sigma weight residual 113.23 107.35 5.88 1.24e+00 6.50e-01 2.25e+01 ... (remaining 10954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 4361 25.08 - 50.15: 344 50.15 - 75.23: 38 75.23 - 100.31: 2 100.31 - 125.39: 10 Dihedral angle restraints: 4755 sinusoidal: 1805 harmonic: 2950 Sorted by residual: dihedral pdb=" CA ASP B 186 " pdb=" CB ASP B 186 " pdb=" CG ASP B 186 " pdb=" OD1 ASP B 186 " ideal model delta sinusoidal sigma weight residual 70.00 175.51 -105.51 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" C25 KHF R 601 " pdb=" C27 KHF R 601 " pdb=" N4 KHF R 601 " pdb=" C29 KHF R 601 " ideal model delta sinusoidal sigma weight residual 116.77 -117.84 -125.39 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C28 KHF R 601 " pdb=" C27 KHF R 601 " pdb=" N4 KHF R 601 " pdb=" C4 KHF R 601 " ideal model delta sinusoidal sigma weight residual -64.48 60.62 -125.10 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 4752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 993 0.045 - 0.090: 181 0.090 - 0.135: 57 0.135 - 0.180: 2 0.180 - 0.225: 4 Chirality restraints: 1237 Sorted by residual: chirality pdb=" CA LEU B 190 " pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CB LEU B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL R 243 " pdb=" N VAL R 243 " pdb=" C VAL R 243 " pdb=" CB VAL R 243 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1234 not shown) Planarity restraints: 1387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C THR B 87 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 332 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 145 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C TYR B 145 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR B 145 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU B 146 " 0.008 2.00e-02 2.50e+03 ... (remaining 1384 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1471 2.77 - 3.30: 7376 3.30 - 3.84: 13547 3.84 - 4.37: 15152 4.37 - 4.90: 26951 Nonbonded interactions: 64497 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.240 3.040 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.247 3.040 nonbonded pdb=" O VAL R 423 " pdb=" OG1 THR R 427 " model vdw 2.254 3.040 nonbonded pdb=" O THR A 325 " pdb=" OG1 THR A 325 " model vdw 2.260 3.040 nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.305 3.040 ... (remaining 64492 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.005 0.184 8067 Z= 0.265 Angle : 0.682 22.198 10965 Z= 0.351 Chirality : 0.040 0.225 1237 Planarity : 0.003 0.041 1387 Dihedral : 17.649 125.387 2838 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.24 % Allowed : 24.85 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.27), residues: 994 helix: 2.79 (0.26), residues: 400 sheet: 0.86 (0.36), residues: 206 loop : -0.32 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 15 TYR 0.009 0.001 TYR R 191 PHE 0.014 0.001 PHE R 238 TRP 0.007 0.001 TRP A 234 HIS 0.004 0.000 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8064) covalent geometry : angle 0.64888 (10959) SS BOND : bond 0.04094 ( 3) SS BOND : angle 8.96224 ( 6) hydrogen bonds : bond 0.18580 ( 416) hydrogen bonds : angle 6.28979 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.336 Fit side-chains REVERT: A 14 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6317 (pp20) REVERT: A 15 ARG cc_start: 0.6178 (ttt-90) cc_final: 0.5291 (ttm110) REVERT: A 21 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6549 (tptp) REVERT: A 213 GLN cc_start: 0.7928 (mt0) cc_final: 0.7427 (tt0) REVERT: A 221 MET cc_start: 0.7744 (ptp) cc_final: 0.7421 (ttp) REVERT: A 240 ASP cc_start: 0.5941 (p0) cc_final: 0.5721 (p0) REVERT: A 268 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6501 (tp30) REVERT: A 347 ARG cc_start: 0.7238 (ptp90) cc_final: 0.6813 (ptp-170) REVERT: A 380 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7262 (ttm110) REVERT: A 389 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7325 (mtm110) REVERT: B 90 VAL cc_start: 0.7823 (m) cc_final: 0.7602 (p) REVERT: B 97 SER cc_start: 0.7018 (p) cc_final: 0.6716 (t) REVERT: B 155 ASN cc_start: 0.6327 (t0) cc_final: 0.6086 (t0) REVERT: B 226 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 325 MET cc_start: 0.8175 (tpp) cc_final: 0.7852 (tpp) REVERT: N 113 THR cc_start: 0.8213 (p) cc_final: 0.7979 (t) REVERT: R 189 MET cc_start: 0.6914 (tpt) cc_final: 0.6519 (tpp) outliers start: 2 outliers final: 1 residues processed: 198 average time/residue: 0.5233 time to fit residues: 110.5744 Evaluate side-chains 127 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.0050 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 75 GLN B 119 ASN B 176 GLN B 259 GLN B 295 ASN G 44 HIS N 5 GLN N 35 ASN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 467 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.193324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160266 restraints weight = 8677.414| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.58 r_work: 0.3694 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8067 Z= 0.128 Angle : 0.506 5.816 10965 Z= 0.272 Chirality : 0.040 0.132 1237 Planarity : 0.003 0.038 1387 Dihedral : 12.287 126.696 1145 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.77 % Allowed : 21.66 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.27), residues: 994 helix: 3.18 (0.25), residues: 398 sheet: 1.24 (0.34), residues: 204 loop : -0.31 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 15 TYR 0.015 0.001 TYR A 339 PHE 0.013 0.001 PHE A 363 TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8064) covalent geometry : angle 0.50414 (10959) SS BOND : bond 0.00734 ( 3) SS BOND : angle 1.89998 ( 6) hydrogen bonds : bond 0.03732 ( 416) hydrogen bonds : angle 4.37197 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.334 Fit side-chains REVERT: A 14 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6780 (pp20) REVERT: A 15 ARG cc_start: 0.6535 (ttt-90) cc_final: 0.6092 (ttp80) REVERT: A 21 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7418 (pptt) REVERT: A 213 GLN cc_start: 0.8426 (mt0) cc_final: 0.7945 (tt0) REVERT: A 240 ASP cc_start: 0.6794 (p0) cc_final: 0.6546 (p0) REVERT: A 299 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6853 (mm-30) REVERT: A 389 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7689 (mtm110) REVERT: B 97 SER cc_start: 0.7562 (p) cc_final: 0.7276 (t) REVERT: B 197 ARG cc_start: 0.7247 (tpp-160) cc_final: 0.6665 (mmt90) REVERT: G 37 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7473 (mt) REVERT: N 34 MET cc_start: 0.8346 (mmm) cc_final: 0.7840 (mmm) REVERT: N 70 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7960 (tt) REVERT: N 73 ASP cc_start: 0.6801 (t70) cc_final: 0.6588 (t70) REVERT: N 113 THR cc_start: 0.8501 (p) cc_final: 0.8270 (m) REVERT: R 189 MET cc_start: 0.6624 (tpt) cc_final: 0.6211 (tpp) REVERT: R 410 THR cc_start: 0.8574 (t) cc_final: 0.8357 (m) outliers start: 39 outliers final: 7 residues processed: 164 average time/residue: 0.5879 time to fit residues: 102.2774 Evaluate side-chains 131 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 264 ASN A 271 ASN B 259 GLN N 5 GLN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN R 467 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.185515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152699 restraints weight = 8589.315| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.57 r_work: 0.3620 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8067 Z= 0.128 Angle : 0.495 5.442 10965 Z= 0.266 Chirality : 0.040 0.146 1237 Planarity : 0.003 0.042 1387 Dihedral : 13.088 157.983 1142 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.77 % Allowed : 20.93 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.27), residues: 994 helix: 3.23 (0.25), residues: 398 sheet: 1.14 (0.34), residues: 208 loop : -0.38 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.014 0.001 TYR A 339 PHE 0.011 0.001 PHE A 363 TRP 0.011 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8064) covalent geometry : angle 0.49421 (10959) SS BOND : bond 0.00290 ( 3) SS BOND : angle 1.57929 ( 6) hydrogen bonds : bond 0.03672 ( 416) hydrogen bonds : angle 4.18089 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.277 Fit side-chains REVERT: A 14 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7013 (pp20) REVERT: A 21 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7581 (pptt) REVERT: A 24 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: A 268 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7384 (tp30) REVERT: A 299 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7175 (mm-30) REVERT: A 389 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7838 (mtm110) REVERT: B 197 ARG cc_start: 0.7299 (tpp-160) cc_final: 0.6700 (mmt90) REVERT: R 189 MET cc_start: 0.6655 (tpt) cc_final: 0.6192 (tpp) REVERT: R 410 THR cc_start: 0.8785 (t) cc_final: 0.8505 (m) outliers start: 39 outliers final: 11 residues processed: 166 average time/residue: 0.5732 time to fit residues: 101.0720 Evaluate side-chains 128 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 307 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 0.0050 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 259 GLN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.184440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152433 restraints weight = 8817.266| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.46 r_work: 0.3619 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8067 Z= 0.113 Angle : 0.479 5.822 10965 Z= 0.256 Chirality : 0.040 0.145 1237 Planarity : 0.003 0.044 1387 Dihedral : 13.005 151.614 1142 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.79 % Allowed : 21.91 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.27), residues: 994 helix: 3.30 (0.25), residues: 398 sheet: 1.29 (0.34), residues: 204 loop : -0.35 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.012 0.001 TYR R 297 PHE 0.011 0.001 PHE R 327 TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8064) covalent geometry : angle 0.47852 (10959) SS BOND : bond 0.00439 ( 3) SS BOND : angle 1.32135 ( 6) hydrogen bonds : bond 0.03322 ( 416) hydrogen bonds : angle 4.03310 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.303 Fit side-chains REVERT: A 14 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7089 (pp20) REVERT: A 21 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7333 (tptp) REVERT: A 268 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7365 (tp30) REVERT: A 283 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7272 (mtt180) REVERT: A 347 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7783 (ttp-110) REVERT: A 389 ARG cc_start: 0.8149 (tpp-160) cc_final: 0.7870 (mtm110) REVERT: B 197 ARG cc_start: 0.7290 (tpp-160) cc_final: 0.6758 (mmt90) REVERT: B 228 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: B 314 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7986 (ptt180) REVERT: N 3 GLN cc_start: 0.7707 (pt0) cc_final: 0.7444 (pt0) REVERT: N 20 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7236 (pp) REVERT: R 189 MET cc_start: 0.6681 (tpt) cc_final: 0.6230 (tpp) REVERT: R 410 THR cc_start: 0.8756 (t) cc_final: 0.8421 (m) outliers start: 31 outliers final: 12 residues processed: 140 average time/residue: 0.6118 time to fit residues: 90.6701 Evaluate side-chains 126 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 307 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 20 optimal weight: 0.0470 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- 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 A 279 ASN A 390 GLN B 75 GLN B 259 GLN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148808 restraints weight = 8676.478| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.50 r_work: 0.3585 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8067 Z= 0.138 Angle : 0.521 8.253 10965 Z= 0.277 Chirality : 0.041 0.149 1237 Planarity : 0.003 0.046 1387 Dihedral : 12.656 166.448 1142 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.79 % Allowed : 21.54 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.27), residues: 994 helix: 3.23 (0.26), residues: 398 sheet: 1.13 (0.34), residues: 214 loop : -0.41 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.015 0.002 TYR R 297 PHE 0.012 0.001 PHE R 327 TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8064) covalent geometry : angle 0.52031 (10959) SS BOND : bond 0.00326 ( 3) SS BOND : angle 1.44782 ( 6) hydrogen bonds : bond 0.03625 ( 416) hydrogen bonds : angle 4.14653 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.331 Fit side-chains REVERT: A 15 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6769 (ttt-90) REVERT: A 21 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7650 (pptt) REVERT: A 28 GLN cc_start: 0.7650 (mt0) cc_final: 0.7364 (mm-40) REVERT: A 55 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5766 (pp) REVERT: A 268 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7406 (tp30) REVERT: A 283 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7250 (mtt180) REVERT: A 389 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7847 (mtm110) REVERT: B 146 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8566 (mm) REVERT: B 196 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7290 (p) REVERT: B 197 ARG cc_start: 0.7291 (tpp-160) cc_final: 0.6787 (mmt90) REVERT: B 314 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8087 (ptt180) REVERT: N 3 GLN cc_start: 0.7624 (pt0) cc_final: 0.7393 (pt0) REVERT: N 20 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7487 (pp) REVERT: R 189 MET cc_start: 0.6693 (tpt) cc_final: 0.6284 (tpp) outliers start: 31 outliers final: 14 residues processed: 151 average time/residue: 0.6051 time to fit residues: 96.7880 Evaluate side-chains 136 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 416 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 264 ASN A 279 ASN B 259 GLN N 31 ASN ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.178055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145028 restraints weight = 8564.889| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.47 r_work: 0.3535 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8067 Z= 0.209 Angle : 0.612 7.096 10965 Z= 0.327 Chirality : 0.044 0.157 1237 Planarity : 0.004 0.048 1387 Dihedral : 12.747 160.406 1142 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.77 % Allowed : 20.69 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.27), residues: 994 helix: 2.90 (0.25), residues: 397 sheet: 0.89 (0.34), residues: 208 loop : -0.48 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 476 TYR 0.020 0.002 TYR R 297 PHE 0.014 0.002 PHE R 327 TRP 0.016 0.002 TRP A 234 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 8064) covalent geometry : angle 0.61056 (10959) SS BOND : bond 0.00338 ( 3) SS BOND : angle 1.65453 ( 6) hydrogen bonds : bond 0.04333 ( 416) hydrogen bonds : angle 4.42783 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.324 Fit side-chains REVERT: A 15 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6734 (ttt-90) REVERT: A 21 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7566 (pptt) REVERT: A 28 GLN cc_start: 0.7744 (mt0) cc_final: 0.7319 (mp10) REVERT: A 55 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5890 (pp) REVERT: A 220 HIS cc_start: 0.8496 (m170) cc_final: 0.8222 (m-70) REVERT: A 268 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7425 (tt0) REVERT: A 374 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8349 (mtt180) REVERT: A 389 ARG cc_start: 0.8095 (tpp-160) cc_final: 0.7775 (mtm110) REVERT: B 65 THR cc_start: 0.8108 (m) cc_final: 0.7862 (p) REVERT: B 76 ASP cc_start: 0.8438 (p0) cc_final: 0.8189 (p0) REVERT: B 146 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8631 (mm) REVERT: B 196 THR cc_start: 0.7617 (OUTLIER) cc_final: 0.7385 (p) REVERT: B 197 ARG cc_start: 0.7338 (tpp-160) cc_final: 0.6758 (mmt90) REVERT: B 314 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8183 (ptt180) REVERT: N 20 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7516 (pp) REVERT: R 189 MET cc_start: 0.6632 (tpt) cc_final: 0.6203 (tpp) outliers start: 39 outliers final: 17 residues processed: 149 average time/residue: 0.6336 time to fit residues: 99.7699 Evaluate side-chains 135 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 59 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN B 259 GLN ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.180598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148285 restraints weight = 8562.190| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.49 r_work: 0.3572 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8067 Z= 0.129 Angle : 0.520 6.051 10965 Z= 0.277 Chirality : 0.040 0.147 1237 Planarity : 0.003 0.047 1387 Dihedral : 12.429 151.520 1142 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.28 % Allowed : 21.79 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.27), residues: 994 helix: 3.10 (0.26), residues: 397 sheet: 0.91 (0.34), residues: 205 loop : -0.53 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.015 0.001 TYR R 297 PHE 0.012 0.001 PHE R 327 TRP 0.015 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8064) covalent geometry : angle 0.51915 (10959) SS BOND : bond 0.00290 ( 3) SS BOND : angle 1.38618 ( 6) hydrogen bonds : bond 0.03550 ( 416) hydrogen bonds : angle 4.15937 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.287 Fit side-chains REVERT: A 15 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6825 (ttt-90) REVERT: A 21 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7898 (mptt) REVERT: A 28 GLN cc_start: 0.7829 (mt0) cc_final: 0.7469 (mp10) REVERT: A 55 ILE cc_start: 0.6275 (OUTLIER) cc_final: 0.5973 (pt) REVERT: A 220 HIS cc_start: 0.8472 (m170) cc_final: 0.8223 (m-70) REVERT: A 370 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: B 65 THR cc_start: 0.8018 (m) cc_final: 0.7807 (p) REVERT: B 197 ARG cc_start: 0.7343 (tpp-160) cc_final: 0.6815 (mmt90) REVERT: B 314 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8117 (ptt180) REVERT: N 20 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7547 (pp) REVERT: R 189 MET cc_start: 0.6679 (tpt) cc_final: 0.6241 (tpp) outliers start: 35 outliers final: 15 residues processed: 143 average time/residue: 0.6437 time to fit residues: 97.2978 Evaluate side-chains 135 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 75 GLN B 259 GLN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148373 restraints weight = 8590.852| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.43 r_work: 0.3578 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8067 Z= 0.131 Angle : 0.518 6.213 10965 Z= 0.276 Chirality : 0.041 0.148 1237 Planarity : 0.003 0.048 1387 Dihedral : 12.198 138.052 1142 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.94 % Allowed : 22.28 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.27), residues: 994 helix: 3.08 (0.25), residues: 398 sheet: 0.81 (0.34), residues: 211 loop : -0.47 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.015 0.001 TYR R 297 PHE 0.012 0.001 PHE R 327 TRP 0.016 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8064) covalent geometry : angle 0.51718 (10959) SS BOND : bond 0.00295 ( 3) SS BOND : angle 1.30469 ( 6) hydrogen bonds : bond 0.03529 ( 416) hydrogen bonds : angle 4.11958 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.322 Fit side-chains REVERT: A 15 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6711 (ttt-90) REVERT: A 21 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7778 (mptt) REVERT: A 28 GLN cc_start: 0.7750 (mt0) cc_final: 0.7314 (mp10) REVERT: A 55 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.6041 (pt) REVERT: A 220 HIS cc_start: 0.8445 (m170) cc_final: 0.8180 (m-70) REVERT: A 370 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: B 65 THR cc_start: 0.7992 (m) cc_final: 0.7733 (p) REVERT: B 197 ARG cc_start: 0.7266 (tpp-160) cc_final: 0.6631 (mmt90) REVERT: B 314 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8157 (ptt180) REVERT: N 20 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7427 (pp) REVERT: R 189 MET cc_start: 0.6649 (tpt) cc_final: 0.6229 (tpp) outliers start: 24 outliers final: 13 residues processed: 137 average time/residue: 0.6192 time to fit residues: 89.7637 Evaluate side-chains 132 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 75 GLN B 259 GLN R 307 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145445 restraints weight = 8557.189| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.53 r_work: 0.3553 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8067 Z= 0.129 Angle : 0.516 6.471 10965 Z= 0.274 Chirality : 0.041 0.148 1237 Planarity : 0.003 0.048 1387 Dihedral : 12.027 127.568 1142 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.82 % Allowed : 23.13 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.27), residues: 994 helix: 3.10 (0.25), residues: 398 sheet: 0.87 (0.34), residues: 209 loop : -0.45 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.014 0.001 TYR R 297 PHE 0.012 0.001 PHE R 327 TRP 0.015 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8064) covalent geometry : angle 0.51509 (10959) SS BOND : bond 0.00302 ( 3) SS BOND : angle 1.27677 ( 6) hydrogen bonds : bond 0.03491 ( 416) hydrogen bonds : angle 4.08011 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.329 Fit side-chains REVERT: A 15 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6881 (ttt-90) REVERT: A 21 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7923 (mptt) REVERT: A 28 GLN cc_start: 0.7831 (mt0) cc_final: 0.7437 (mp10) REVERT: A 55 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.6055 (pt) REVERT: A 220 HIS cc_start: 0.8460 (m170) cc_final: 0.8214 (m-70) REVERT: A 370 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: B 65 THR cc_start: 0.7987 (m) cc_final: 0.7759 (p) REVERT: B 197 ARG cc_start: 0.7397 (tpp-160) cc_final: 0.6774 (mmt90) REVERT: B 314 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8163 (ptt180) REVERT: N 20 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7490 (pp) REVERT: R 189 MET cc_start: 0.6647 (tpt) cc_final: 0.6194 (tpp) REVERT: R 355 SER cc_start: 0.7963 (m) cc_final: 0.7683 (t) outliers start: 23 outliers final: 16 residues processed: 136 average time/residue: 0.6152 time to fit residues: 88.6736 Evaluate side-chains 135 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 259 GLN R 307 HIS R 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.180643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147935 restraints weight = 8534.977| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.50 r_work: 0.3605 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8067 Z= 0.111 Angle : 0.498 6.878 10965 Z= 0.265 Chirality : 0.040 0.176 1237 Planarity : 0.003 0.048 1387 Dihedral : 11.943 127.258 1142 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.33 % Allowed : 23.75 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.27), residues: 994 helix: 3.15 (0.26), residues: 398 sheet: 0.94 (0.34), residues: 205 loop : -0.49 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.013 0.001 TYR R 297 PHE 0.012 0.001 PHE R 327 TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8064) covalent geometry : angle 0.49702 (10959) SS BOND : bond 0.00274 ( 3) SS BOND : angle 1.15166 ( 6) hydrogen bonds : bond 0.03310 ( 416) hydrogen bonds : angle 4.01385 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.394 Fit side-chains REVERT: A 21 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7743 (mptt) REVERT: A 28 GLN cc_start: 0.7744 (mt0) cc_final: 0.7302 (mp10) REVERT: A 51 LYS cc_start: 0.7505 (mmtm) cc_final: 0.7221 (mttt) REVERT: A 55 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.6065 (pt) REVERT: A 220 HIS cc_start: 0.8447 (m170) cc_final: 0.8206 (m-70) REVERT: A 370 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: B 65 THR cc_start: 0.7908 (m) cc_final: 0.7663 (p) REVERT: B 197 ARG cc_start: 0.7273 (tpp-160) cc_final: 0.6649 (mmt90) REVERT: B 314 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8120 (ptt180) REVERT: N 20 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7420 (pp) REVERT: R 189 MET cc_start: 0.6621 (tpt) cc_final: 0.6178 (tpp) REVERT: R 355 SER cc_start: 0.7987 (m) cc_final: 0.7678 (t) REVERT: R 414 MET cc_start: 0.7259 (ptm) cc_final: 0.6958 (ptt) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.6148 time to fit residues: 86.8106 Evaluate side-chains 132 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 259 GLN R 307 HIS R 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145071 restraints weight = 8567.008| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.41 r_work: 0.3517 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8067 Z= 0.173 Angle : 0.566 7.110 10965 Z= 0.302 Chirality : 0.043 0.166 1237 Planarity : 0.004 0.048 1387 Dihedral : 12.052 127.617 1142 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.69 % Allowed : 23.26 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.27), residues: 994 helix: 2.95 (0.25), residues: 398 sheet: 0.72 (0.34), residues: 212 loop : -0.48 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 96 TYR 0.018 0.002 TYR R 297 PHE 0.014 0.002 PHE R 327 TRP 0.016 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8064) covalent geometry : angle 0.56545 (10959) SS BOND : bond 0.00327 ( 3) SS BOND : angle 1.36017 ( 6) hydrogen bonds : bond 0.03915 ( 416) hydrogen bonds : angle 4.23148 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3782.45 seconds wall clock time: 65 minutes 13.39 seconds (3913.39 seconds total)