Starting phenix.real_space_refine on Sun May 11 09:01:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jr9_36593/05_2025/8jr9_36593_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jr9_36593/05_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_36593/05_2025/8jr9_36593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jr9_36593/05_2025/8jr9_36593.map" model { file = "/net/cci-nas-00/data/ceres_data/8jr9_36593/05_2025/8jr9_36593_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jr9_36593/05_2025/8jr9_36593_neut_trim.cif" } resolution = 2.57 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ARG:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 7, '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, 'GLU:plan': 1, 'ARG: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: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 6, '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: 5.09, per 1000 atoms: 0.64 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: 1.98 Conformation dependent library (CDL) restraints added in 907.1 milliseconds 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: 1.05 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: 2.51 Time building geometry restraints manager: 2.26 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 21.220 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.200 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (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 TRP 0.007 0.001 TRP A 234 HIS 0.004 0.000 HIS A 387 PHE 0.014 0.001 PHE R 238 TYR 0.009 0.001 TYR R 191 ARG 0.007 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.18580 ( 416) hydrogen bonds : angle 6.28979 ( 1191) SS BOND : bond 0.04094 ( 3) SS BOND : angle 8.96224 ( 6) covalent geometry : bond 0.00465 ( 8064) covalent geometry : angle 0.64888 (10959) *********************** 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 : 0.903 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: 0.5290 (ttm110) REVERT: A 21 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6548 (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: 0.5720 (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: 0.7263 (ttm110) REVERT: A 389 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7326 (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: 0.7037 (mt-10) REVERT: B 325 MET cc_start: 0.8175 (tpp) cc_final: 0.7853 (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: 0.9490 time to fit residues: 201.3395 Evaluate side-chains 126 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 83 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.190094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154982 restraints weight = 8559.709| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.55 r_work: 0.3664 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2279 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= 0.143 Angle : 0.532 6.168 10965 Z= 0.284 Chirality : 0.041 0.135 1237 Planarity : 0.004 0.037 1387 Dihedral : 12.255 126.431 1145 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.65 % Allowed : 21.18 % Favored : 74.17 % 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: 2.16 (0.27), residues: 994 helix: 3.14 (0.25), residues: 398 sheet: 1.21 (0.34), residues: 206 loop : -0.29 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.008 0.001 HIS A 357 PHE 0.015 0.002 PHE A 363 TYR 0.018 0.002 TYR A 339 ARG 0.005 0.001 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 416) hydrogen bonds : angle 4.41117 ( 1191) SS BOND : bond 0.00566 ( 3) SS BOND : angle 1.88470 ( 6) covalent geometry : bond 0.00312 ( 8064) covalent geometry : angle 0.53030 (10959) *********************** 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 181 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.931 Fit side-chains REVERT: A 14 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6879 (pp20) REVERT: A 15 ARG cc_start: 0.6571 (ttt-90) cc_final: 0.6116 (ttp80) REVERT: A 21 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7263 (pptt) REVERT: A 25 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7173 (mttp) REVERT: A 213 GLN cc_start: 0.8545 (mt0) cc_final: 0.8069 (tt0) REVERT: A 240 ASP cc_start: 0.6866 (p0) cc_final: 0.6614 (p0) REVERT: A 299 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6912 (mm-30) REVERT: A 370 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: A 389 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7706 (mtm110) REVERT: B 97 SER cc_start: 0.7753 (p) cc_final: 0.7480 (t) REVERT: B 197 ARG cc_start: 0.7267 (tpp-160) cc_final: 0.6639 (mmt90) REVERT: G 37 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7434 (mt) REVERT: N 34 MET cc_start: 0.8359 (mmm) cc_final: 0.7861 (mmm) REVERT: N 70 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8059 (tt) REVERT: N 73 ASP cc_start: 0.6857 (t70) cc_final: 0.6644 (t70) REVERT: R 189 MET cc_start: 0.6612 (tpt) cc_final: 0.6207 (tpp) REVERT: R 410 THR cc_start: 0.8704 (t) cc_final: 0.8446 (m) outliers start: 38 outliers final: 8 residues processed: 169 average time/residue: 1.0875 time to fit residues: 195.6121 Evaluate side-chains 133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER 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 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 12 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 5 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 = 0.4109 r_free = 0.4109 target = 0.184887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150944 restraints weight = 8732.084| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.51 r_work: 0.3615 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3026 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= 0.124 Angle : 0.497 8.946 10965 Z= 0.266 Chirality : 0.040 0.137 1237 Planarity : 0.003 0.042 1387 Dihedral : 12.217 127.337 1142 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.16 % Allowed : 22.52 % Favored : 73.32 % 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: 2.20 (0.27), residues: 994 helix: 3.23 (0.25), residues: 398 sheet: 1.18 (0.34), residues: 206 loop : -0.31 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE A 363 TYR 0.013 0.001 TYR A 339 ARG 0.005 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 416) hydrogen bonds : angle 4.17662 ( 1191) SS BOND : bond 0.00880 ( 3) SS BOND : angle 1.75108 ( 6) covalent geometry : bond 0.00271 ( 8064) covalent geometry : angle 0.49583 (10959) *********************** 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 164 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.939 Fit side-chains REVERT: A 14 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6990 (pp20) REVERT: A 21 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7487 (pptt) REVERT: A 24 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7014 (mp10) REVERT: A 25 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7482 (mttp) REVERT: A 240 ASP cc_start: 0.7179 (p0) cc_final: 0.6970 (p0) REVERT: A 268 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7346 (tp30) REVERT: A 389 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.7832 (mtm110) REVERT: B 170 ASP cc_start: 0.7655 (p0) cc_final: 0.7418 (p0) REVERT: B 197 ARG cc_start: 0.7310 (tpp-160) cc_final: 0.6786 (mmt90) REVERT: N 20 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7164 (pp) REVERT: R 189 MET cc_start: 0.6664 (tpt) cc_final: 0.6193 (tpp) REVERT: R 410 THR cc_start: 0.8764 (t) cc_final: 0.8482 (m) outliers start: 34 outliers final: 14 residues processed: 152 average time/residue: 1.1109 time to fit residues: 180.1101 Evaluate side-chains 129 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 47 SER 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 142 HIS Chi-restraints excluded: chain B residue 196 THR 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 73 ASP Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 224 MET 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 59 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 259 GLN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145216 restraints weight = 8651.652| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.55 r_work: 0.3562 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8067 Z= 0.134 Angle : 0.511 7.056 10965 Z= 0.272 Chirality : 0.041 0.137 1237 Planarity : 0.003 0.045 1387 Dihedral : 12.165 127.510 1142 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.04 % Allowed : 21.42 % 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 (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: 2.16 (0.27), residues: 994 helix: 3.24 (0.26), residues: 398 sheet: 1.19 (0.34), residues: 210 loop : -0.41 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 327 TYR 0.014 0.002 TYR A 339 ARG 0.006 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 416) hydrogen bonds : angle 4.13113 ( 1191) SS BOND : bond 0.00098 ( 3) SS BOND : angle 1.51621 ( 6) covalent geometry : bond 0.00295 ( 8064) covalent geometry : angle 0.50995 (10959) *********************** 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 161 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.818 Fit side-chains REVERT: A 15 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6762 (ttt-90) REVERT: A 21 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7461 (mptt) REVERT: A 25 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7699 (mttp) REVERT: A 28 GLN cc_start: 0.7630 (mt0) cc_final: 0.7274 (mm-40) REVERT: A 268 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7263 (tp30) REVERT: A 370 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: A 389 ARG cc_start: 0.8130 (tpp-160) cc_final: 0.7787 (mtm110) REVERT: B 197 ARG cc_start: 0.7322 (tpp-160) cc_final: 0.6765 (mmt90) REVERT: B 314 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8039 (ptt180) REVERT: N 3 GLN cc_start: 0.7651 (pt0) cc_final: 0.7406 (pt0) REVERT: N 20 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7349 (pp) REVERT: R 189 MET cc_start: 0.6625 (tpt) cc_final: 0.6201 (tpp) REVERT: R 312 MET cc_start: 0.7032 (ptp) cc_final: 0.6773 (ptp) REVERT: R 410 THR cc_start: 0.8820 (t) cc_final: 0.8493 (m) REVERT: R 414 MET cc_start: 0.7331 (ptt) cc_final: 0.6855 (ttm) outliers start: 33 outliers final: 16 residues processed: 154 average time/residue: 1.0689 time to fit residues: 175.3687 Evaluate side-chains 137 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 142 HIS 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 198 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 94 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 390 GLN B 75 GLN B 259 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.180393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144376 restraints weight = 8604.481| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.55 r_work: 0.3559 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3882 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= 0.133 Angle : 0.510 6.846 10965 Z= 0.273 Chirality : 0.040 0.152 1237 Planarity : 0.003 0.046 1387 Dihedral : 12.099 127.570 1142 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.65 % Allowed : 20.32 % Favored : 75.03 % 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: 2.14 (0.27), residues: 994 helix: 3.21 (0.26), residues: 398 sheet: 1.24 (0.34), residues: 209 loop : -0.45 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 327 TYR 0.015 0.001 TYR R 297 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 416) hydrogen bonds : angle 4.10820 ( 1191) SS BOND : bond 0.00350 ( 3) SS BOND : angle 1.41310 ( 6) covalent geometry : bond 0.00297 ( 8064) covalent geometry : angle 0.50927 (10959) *********************** 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 162 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.882 Fit side-chains REVERT: A 21 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7311 (tptp) REVERT: A 28 GLN cc_start: 0.7647 (mt0) cc_final: 0.7250 (mm-40) REVERT: A 55 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5722 (pp) REVERT: A 268 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7289 (tp30) REVERT: A 370 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: A 389 ARG cc_start: 0.8085 (tpp-160) cc_final: 0.7761 (mtm110) REVERT: B 146 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8499 (mm) REVERT: B 196 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7241 (p) REVERT: B 197 ARG cc_start: 0.7267 (tpp-160) cc_final: 0.6728 (mmt90) REVERT: B 291 ASP cc_start: 0.7722 (p0) cc_final: 0.7503 (p0) REVERT: B 314 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8060 (ptt180) REVERT: N 3 GLN cc_start: 0.7577 (pt0) cc_final: 0.7362 (pt0) REVERT: N 20 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7403 (pp) REVERT: R 189 MET cc_start: 0.6646 (tpt) cc_final: 0.6253 (tpp) REVERT: R 198 SER cc_start: 0.7161 (OUTLIER) cc_final: 0.6565 (m) REVERT: R 414 MET cc_start: 0.7331 (ptt) cc_final: 0.6844 (ttm) outliers start: 38 outliers final: 16 residues processed: 151 average time/residue: 1.0983 time to fit residues: 176.2367 Evaluate side-chains 135 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 135 VAL Chi-restraints excluded: chain B residue 142 HIS 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 52 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 0.0050 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 B 259 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.180283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143937 restraints weight = 8566.870| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.55 r_work: 0.3536 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4160 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= 0.153 Angle : 0.544 6.235 10965 Z= 0.291 Chirality : 0.041 0.154 1237 Planarity : 0.004 0.047 1387 Dihedral : 12.081 127.723 1142 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.77 % Allowed : 20.44 % 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 (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: 2.06 (0.27), residues: 994 helix: 3.13 (0.26), residues: 397 sheet: 1.10 (0.34), residues: 214 loop : -0.42 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.013 0.001 PHE R 327 TYR 0.016 0.002 TYR R 297 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 416) hydrogen bonds : angle 4.21068 ( 1191) SS BOND : bond 0.00152 ( 3) SS BOND : angle 1.50514 ( 6) covalent geometry : bond 0.00345 ( 8064) covalent geometry : angle 0.54323 (10959) *********************** 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 157 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.907 Fit side-chains REVERT: A 21 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7780 (mptt) REVERT: A 28 GLN cc_start: 0.7783 (mt0) cc_final: 0.7317 (mp10) REVERT: A 55 ILE cc_start: 0.6197 (OUTLIER) cc_final: 0.5894 (pt) REVERT: A 268 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7564 (tt0) REVERT: A 370 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: A 374 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8352 (mtt180) REVERT: A 389 ARG cc_start: 0.8094 (tpp-160) cc_final: 0.7781 (mtm110) REVERT: B 65 THR cc_start: 0.8019 (m) cc_final: 0.7770 (p) REVERT: B 146 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 196 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.7331 (p) REVERT: B 197 ARG cc_start: 0.7349 (tpp-160) cc_final: 0.6715 (mmt90) REVERT: B 314 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8134 (ptt180) REVERT: N 20 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7484 (pp) REVERT: R 187 LEU cc_start: 0.4738 (OUTLIER) cc_final: 0.4472 (mt) REVERT: R 189 MET cc_start: 0.6582 (tpt) cc_final: 0.6145 (tpp) REVERT: R 198 SER cc_start: 0.7171 (OUTLIER) cc_final: 0.6616 (m) outliers start: 39 outliers final: 16 residues processed: 144 average time/residue: 1.1220 time to fit residues: 172.0015 Evaluate side-chains 135 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 142 HIS 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 215 GLU 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 187 LEU Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 HIS 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 59 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.181223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145178 restraints weight = 8513.364| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.54 r_work: 0.3548 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8067 Z= 0.134 Angle : 0.523 6.035 10965 Z= 0.279 Chirality : 0.040 0.150 1237 Planarity : 0.003 0.047 1387 Dihedral : 11.862 127.520 1142 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.92 % Allowed : 20.93 % Favored : 75.15 % 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: 2.05 (0.27), residues: 994 helix: 3.11 (0.26), residues: 398 sheet: 1.08 (0.34), residues: 212 loop : -0.40 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 327 TYR 0.015 0.001 TYR R 297 ARG 0.002 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 416) hydrogen bonds : angle 4.12553 ( 1191) SS BOND : bond 0.00306 ( 3) SS BOND : angle 1.34682 ( 6) covalent geometry : bond 0.00303 ( 8064) covalent geometry : angle 0.52213 (10959) *********************** 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 147 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.831 Fit side-chains REVERT: A 21 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7787 (mptt) REVERT: A 28 GLN cc_start: 0.7774 (mt0) cc_final: 0.7311 (mp10) REVERT: A 55 ILE cc_start: 0.6224 (OUTLIER) cc_final: 0.5938 (pt) REVERT: A 220 HIS cc_start: 0.8494 (m170) cc_final: 0.8255 (m-70) REVERT: A 268 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7532 (tt0) REVERT: A 370 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: A 374 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8349 (mtt180) REVERT: A 389 ARG cc_start: 0.8071 (tpp-160) cc_final: 0.7766 (mtm110) REVERT: B 65 THR cc_start: 0.8001 (m) cc_final: 0.7751 (p) REVERT: B 196 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7347 (p) REVERT: B 197 ARG cc_start: 0.7319 (tpp-160) cc_final: 0.6694 (mmt90) REVERT: B 314 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8132 (ptt180) REVERT: N 20 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7442 (pp) REVERT: R 187 LEU cc_start: 0.4719 (OUTLIER) cc_final: 0.4445 (mt) REVERT: R 189 MET cc_start: 0.6583 (tpt) cc_final: 0.6144 (tpp) REVERT: R 198 SER cc_start: 0.7270 (OUTLIER) cc_final: 0.6654 (m) outliers start: 32 outliers final: 17 residues processed: 139 average time/residue: 1.1057 time to fit residues: 163.3370 Evaluate side-chains 138 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 142 HIS 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 52 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 198 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 59 optimal weight: 8.9990 chunk 87 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.182301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147078 restraints weight = 8556.957| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.49 r_work: 0.3575 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8067 Z= 0.114 Angle : 0.500 6.188 10965 Z= 0.266 Chirality : 0.040 0.160 1237 Planarity : 0.003 0.047 1387 Dihedral : 11.643 127.374 1142 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.79 % Allowed : 20.93 % Favored : 75.28 % 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: 2.07 (0.27), residues: 994 helix: 3.18 (0.26), residues: 397 sheet: 1.17 (0.34), residues: 206 loop : -0.47 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.008 0.001 HIS R 307 PHE 0.011 0.001 PHE R 327 TYR 0.013 0.001 TYR R 297 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 416) hydrogen bonds : angle 4.02937 ( 1191) SS BOND : bond 0.00264 ( 3) SS BOND : angle 1.20153 ( 6) covalent geometry : bond 0.00254 ( 8064) covalent geometry : angle 0.49916 (10959) *********************** 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 153 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.926 Fit side-chains REVERT: A 21 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7781 (mptt) REVERT: A 28 GLN cc_start: 0.7753 (mt0) cc_final: 0.7310 (mp10) REVERT: A 55 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5956 (pt) REVERT: A 220 HIS cc_start: 0.8488 (m170) cc_final: 0.8248 (m-70) REVERT: A 370 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: A 374 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8318 (mtt180) REVERT: A 389 ARG cc_start: 0.8009 (tpp-160) cc_final: 0.7723 (mtm110) REVERT: B 65 THR cc_start: 0.7923 (m) cc_final: 0.7666 (p) REVERT: B 197 ARG cc_start: 0.7292 (tpp-160) cc_final: 0.6681 (mmt90) REVERT: B 291 ASP cc_start: 0.7715 (p0) cc_final: 0.7478 (p0) REVERT: B 314 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8145 (ptt180) REVERT: N 20 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7404 (pp) REVERT: R 187 LEU cc_start: 0.4745 (OUTLIER) cc_final: 0.4463 (mt) REVERT: R 189 MET cc_start: 0.6614 (tpt) cc_final: 0.6211 (tpp) outliers start: 31 outliers final: 13 residues processed: 144 average time/residue: 1.0626 time to fit residues: 163.2145 Evaluate side-chains 135 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 A residue 374 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS 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 52 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 HIS R 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.181883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148918 restraints weight = 8661.728| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.51 r_work: 0.3552 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8067 Z= 0.124 Angle : 0.513 6.478 10965 Z= 0.272 Chirality : 0.041 0.159 1237 Planarity : 0.003 0.048 1387 Dihedral : 11.426 127.428 1142 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.94 % Allowed : 21.91 % Favored : 75.15 % 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: 2.07 (0.27), residues: 994 helix: 3.16 (0.26), residues: 397 sheet: 1.11 (0.35), residues: 208 loop : -0.44 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 327 TYR 0.015 0.001 TYR R 297 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 416) hydrogen bonds : angle 4.01944 ( 1191) SS BOND : bond 0.00324 ( 3) SS BOND : angle 1.20549 ( 6) covalent geometry : bond 0.00276 ( 8064) covalent geometry : angle 0.51251 (10959) *********************** 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 145 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.892 Fit side-chains REVERT: A 21 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7904 (mptt) REVERT: A 28 GLN cc_start: 0.7849 (mt0) cc_final: 0.7440 (mp10) REVERT: A 55 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.6008 (pt) REVERT: A 220 HIS cc_start: 0.8485 (m170) cc_final: 0.8233 (m-70) REVERT: A 370 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: A 374 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8390 (mtt180) REVERT: A 389 ARG cc_start: 0.8061 (tpp-160) cc_final: 0.7848 (mtm110) REVERT: B 65 THR cc_start: 0.7930 (m) cc_final: 0.7712 (p) REVERT: B 197 ARG cc_start: 0.7294 (tpp-160) cc_final: 0.6693 (mmt90) REVERT: B 314 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8128 (ptt180) REVERT: N 20 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7458 (pp) REVERT: R 187 LEU cc_start: 0.4826 (OUTLIER) cc_final: 0.4507 (mt) REVERT: R 189 MET cc_start: 0.6609 (tpt) cc_final: 0.6179 (tpp) REVERT: R 355 SER cc_start: 0.7983 (m) cc_final: 0.7691 (t) outliers start: 24 outliers final: 14 residues processed: 140 average time/residue: 1.1432 time to fit residues: 170.4449 Evaluate side-chains 134 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 264 ASN 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 135 VAL Chi-restraints excluded: chain B residue 142 HIS 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 52 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 187 LEU 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 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 17 optimal weight: 0.0070 chunk 8 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 295 ASN R 307 HIS R 364 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.185431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.152856 restraints weight = 8590.124| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.46 r_work: 0.3625 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8067 Z= 0.097 Angle : 0.478 6.719 10965 Z= 0.252 Chirality : 0.039 0.150 1237 Planarity : 0.003 0.048 1387 Dihedral : 11.181 127.066 1142 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.96 % Allowed : 22.52 % Favored : 75.52 % 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: 2.12 (0.27), residues: 994 helix: 3.24 (0.26), residues: 397 sheet: 1.09 (0.35), residues: 207 loop : -0.41 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 387 PHE 0.010 0.001 PHE R 327 TYR 0.017 0.001 TYR N 60 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 416) hydrogen bonds : angle 3.82943 ( 1191) SS BOND : bond 0.00237 ( 3) SS BOND : angle 1.04201 ( 6) covalent geometry : bond 0.00213 ( 8064) covalent geometry : angle 0.47786 (10959) ********************** 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 139 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.821 Fit side-chains REVERT: A 21 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7881 (mptt) REVERT: A 28 GLN cc_start: 0.7845 (mt0) cc_final: 0.7484 (mp10) REVERT: A 55 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.6075 (pt) REVERT: A 268 GLU cc_start: 0.7936 (tt0) cc_final: 0.7470 (tp30) REVERT: B 197 ARG cc_start: 0.7290 (tpp-160) cc_final: 0.6696 (mmt90) REVERT: B 314 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8068 (ptt180) REVERT: R 187 LEU cc_start: 0.4740 (OUTLIER) cc_final: 0.4436 (mt) REVERT: R 189 MET cc_start: 0.6610 (tpt) cc_final: 0.6161 (tpp) REVERT: R 355 SER cc_start: 0.7985 (m) cc_final: 0.7712 (t) REVERT: R 414 MET cc_start: 0.7230 (ptt) cc_final: 0.6798 (ttm) outliers start: 16 outliers final: 11 residues processed: 134 average time/residue: 1.0978 time to fit residues: 156.5864 Evaluate side-chains 130 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 264 ASN Chi-restraints excluded: chain A residue 335 THR 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 25 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 187 LEU 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 89 optimal weight: 0.0170 chunk 55 optimal weight: 0.5980 chunk 63 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 307 HIS R 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.182978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151711 restraints weight = 8584.967| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.42 r_work: 0.3602 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8067 Z= 0.103 Angle : 0.487 6.849 10965 Z= 0.257 Chirality : 0.040 0.154 1237 Planarity : 0.003 0.047 1387 Dihedral : 11.154 127.150 1142 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.96 % Allowed : 22.77 % Favored : 75.28 % 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: 2.13 (0.27), residues: 994 helix: 3.23 (0.26), residues: 397 sheet: 1.11 (0.35), residues: 207 loop : -0.40 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS A 387 PHE 0.018 0.001 PHE B 292 TYR 0.016 0.001 TYR N 80 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 416) hydrogen bonds : angle 3.82692 ( 1191) SS BOND : bond 0.00233 ( 3) SS BOND : angle 1.04545 ( 6) covalent geometry : bond 0.00228 ( 8064) covalent geometry : angle 0.48641 (10959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6777.92 seconds wall clock time: 117 minutes 8.53 seconds (7028.53 seconds total)